gromacs →
2020.4-2 →
armhf → 2020-12-08 21:31:34
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| gromacs 2020.4-2 (armhf) Tue, 08 Dec 2020 18:26:17 +0000 |
+==============================================================================+
Package: gromacs
Version: 2020.4-2
Source Version: 2020.4-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-abc2f364-3fce-46c3-91d6-61f9973e38ed' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.9 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.9 MB in 9s (2764 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'gromacs' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/debichem-team/gromacs.git
Please use:
git clone https://salsa.debian.org/debichem-team/gromacs.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 29.2 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main gromacs 2020.4-2 (dsc) [2587 B]
Get:2 http://172.17.0.1/private bullseye-staging/main gromacs 2020.4-2 (tar) [29.1 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main gromacs 2020.4-2 (diff) [37.5 kB]
Fetched 29.2 MB in 6s (5141 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/gromacs-t2PgYV/gromacs-2020.4' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gromacs-t2PgYV' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-GLGsJF/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-GLGsJF/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-GLGsJF/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-GLGsJF/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-GLGsJF/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-GLGsJF/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-GLGsJF/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-GLGsJF/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (9491 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
bsdextrautils krb5-locales libpam-cap netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 59 not upgraded.
Need to get 856 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-GLGsJF/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 856 B in 0s (66.9 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12762 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: chrpath, cmake, debhelper-compat (= 13), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.10.2-7), libx11-dev, lsb-release, mpich, openmpi-bin, zlib1g-dev
Filtered Build-Depends: chrpath, cmake, debhelper-compat (= 13), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.10.2-7), libx11-dev, lsb-release, mpich, openmpi-bin, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-gromacs-dummy' in '/<<BUILDDIR>>/resolver-GLGsJF/apt_archive/sbuild-build-depends-gromacs-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-gromacs-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-GLGsJF/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-GLGsJF/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-GLGsJF/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-GLGsJF/apt_archive ./ Sources [586 B]
Get:5 copy:/<<BUILDDIR>>/resolver-GLGsJF/apt_archive ./ Packages [668 B]
Fetched 2587 B in 0s (11.6 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install gromacs build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libisl22 libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev chrpath cmake cmake-data cpp-10
debhelper dh-autoreconf dh-strip-nondeterminism distro-info-data dwz file
g++-10 gcc-10 gcc-10-base gettext gettext-base gfortran gfortran-10
groff-base hwloc-nox ibverbs-providers intltool-debian libarchive-zip-perl
libarchive13 libasan6 libatomic1 libblas-dev libblas3 libboost-dev
libboost1.71-dev libbrotli1 libbsd0 libcbor0 libcc1-0 libcroco3 libcurl4
libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7
libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
libevent-pthreads-2.1-7 libexpat1 libfftw3-bin libfftw3-dev libfftw3-double3
libfftw3-single3 libfido2-1 libfile-stripnondeterminism-perl libgcc-10-dev
libgcc-s1 libgfortran-10-dev libgfortran5 libglib2.0-0 libgomp1 libhwloc-dev
libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu67 libisl23
libjs-jquery libjs-jquery-ui libjsoncpp1 liblapack-dev liblapack3
libltdl-dev libltdl7 libmagic-mgc libmagic1 libmpich-dev libmpich12
libncurses6 libncursesw6 libnghttp2-14 libnl-3-200 libnl-3-dev
libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev
libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev libpmix2 libprocps8
libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.9-minimal
libpython3.9-stdlib librhash0 librtmp1 libsigsegv2 libssh2-1
libstdc++-10-dev libstdc++6 libsub-override-perl libtinfo6 libtool libubsan1
libuchardet0 libuv1 libx11-6 libx11-data libx11-dev libxau-dev libxau6
libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext6 libxml2 libxnvctrl0
lsb-release m4 mailcap man-db media-types mime-support mpich node-jquery
ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf
procps python3 python3-minimal python3.9 python3.9-minimal x11proto-core-dev
x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build
gcc-10-locales dh-make gcc-10-doc gettext-doc libasprintf-dev
libgettextpo-dev gfortran-doc gfortran-10-doc libcoarrays-dev groff lrzip
liblapack-doc libboost-doc libboost1.71-doc libboost-atomic1.71-dev
libboost-chrono1.71-dev libboost-container1.71-dev libboost-context1.71-dev
libboost-contract1.71-dev libboost-coroutine1.71-dev
libboost-date-time1.71-dev libboost-exception1.71-dev libboost-fiber1.71-dev
libboost-filesystem1.71-dev libboost-graph1.71-dev
libboost-graph-parallel1.71-dev libboost-iostreams1.71-dev
libboost-locale1.71-dev libboost-log1.71-dev libboost-math1.71-dev
libboost-mpi1.71-dev libboost-mpi-python1.71-dev libboost-numpy1.71-dev
libboost-program-options1.71-dev libboost-python1.71-dev
libboost-random1.71-dev libboost-regex1.71-dev
libboost-serialization1.71-dev libboost-stacktrace1.71-dev
libboost-system1.71-dev libboost-test1.71-dev libboost-thread1.71-dev
libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev
libboost1.71-tools-dev libmpfrc++-dev libntl-dev libfftw3-doc
libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils libstdc++-10-doc
gcj-jdk libx11-doc libxcb-doc m4-doc apparmor less www-browser mpich-doc
opencl-icd keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl
python3-doc python3-tk python3-venv python3.9-venv python3.9-doc
binfmt-support
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs javascript-common libgpm2
libcoarrays-openmpi-dev publicsuffix libjs-sizzle xauth
libmail-sendmail-perl psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev chrpath cmake cmake-data debhelper
dh-autoreconf dh-strip-nondeterminism distro-info-data dwz file gettext
gettext-base gfortran gfortran-10 groff-base hwloc-nox ibverbs-providers
intltool-debian libarchive-zip-perl libarchive13 libblas-dev libblas3
libboost-dev libboost1.71-dev libbrotli1 libbsd0 libcbor0 libcroco3 libcurl4
libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7
libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
libevent-pthreads-2.1-7 libexpat1 libfftw3-bin libfftw3-dev libfftw3-double3
libfftw3-single3 libfido2-1 libfile-stripnondeterminism-perl
libgfortran-10-dev libgfortran5 libglib2.0-0 libhwloc-dev libhwloc-plugins
libhwloc15 libibverbs-dev libibverbs1 libicu67 libisl23 libjs-jquery
libjs-jquery-ui libjsoncpp1 liblapack-dev liblapack3 libltdl-dev libltdl7
libmagic-mgc libmagic1 libmpich-dev libmpich12 libncurses6 libnghttp2-14
libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev
libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev
libpmix2 libprocps8 libpsl5 libpthread-stubs0-dev libpython3-stdlib
libpython3.9-minimal libpython3.9-stdlib librhash0 librtmp1 libsigsegv2
libssh2-1 libsub-override-perl libtool libuchardet0 libuv1 libx11-6
libx11-data libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev
libxdmcp6 libxext6 libxml2 libxnvctrl0 lsb-release m4 mailcap man-db
media-types mime-support mpich node-jquery ocl-icd-libopencl1 openmpi-bin
openmpi-common openssh-client po-debconf procps python3 python3-minimal
python3.9 python3.9-minimal sbuild-build-depends-gromacs-dummy
x11proto-core-dev x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
The following packages will be upgraded:
cpp-10 g++-10 gcc-10 gcc-10-base libasan6 libatomic1 libcc1-0 libgcc-10-dev
libgcc-s1 libgomp1 libncursesw6 libstdc++-10-dev libstdc++6 libtinfo6
libubsan1
15 upgraded, 133 newly installed, 0 to remove and 44 not upgraded.
Need to get 229 MB of archives.
After this operation, 244 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-GLGsJF/apt_archive ./ sbuild-build-depends-gromacs-dummy 0.invalid.0 [960 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libisl23 armhf 0.23-1 [497 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libcc1-0 armhf 10.2.0-19+rpi1 [38.4 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf gcc-10-base armhf 10.2.0-19+rpi1 [200 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libgcc-s1 armhf 10.2.0-19+rpi1 [36.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libgomp1 armhf 10.2.0-19+rpi1 [83.7 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libatomic1 armhf 10.2.0-19+rpi1 [8180 B]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libasan6 armhf 10.2.0-19+rpi1 [300 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libubsan1 armhf 10.2.0-19+rpi1 [115 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf g++-10 armhf 10.2.0-19+rpi1 [41.4 MB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libstdc++-10-dev armhf 10.2.0-19+rpi1 [1751 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libgcc-10-dev armhf 10.2.0-19+rpi1 [682 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf gcc-10 armhf 10.2.0-19+rpi1 [44.4 MB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf cpp-10 armhf 10.2.0-19+rpi1 [38.5 MB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libstdc++6 armhf 10.2.0-19+rpi1 [409 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-minimal armhf 3.9.0-5+rpi1 [788 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-1 [73.3 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf python3.9-minimal armhf 3.9.0-5+rpi1 [1628 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.9.0-4 [37.8 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf media-types all 1.0.1 [18.2 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf mailcap all 3.67 [31.3 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.66 [10.9 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libtinfo6 armhf 6.2+20201114-1 [328 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libncursesw6 armhf 6.2+20201114-1 [105 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-stdlib armhf 3.9.0-5+rpi1 [1654 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf python3.9 armhf 3.9.0-5+rpi1 [455 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.9.0-4 [21.0 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.9.0-4 [64.1 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20201114-1 [79.5 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libprocps8 armhf 2:3.3.16-5 [59.8 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.16-5 [238 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libedit2 armhf 3.1-20191231-1 [79.2 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libcbor0 armhf 0.5.0+dfsg-2 [19.5 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libfido2-1 armhf 1.5.0-2 [46.2 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf openssh-client armhf 1:8.4p1-3+b1 [793 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf cmake-data all 3.18.4-1+rpi1 [1725 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libarchive13 armhf 3.4.3-2 [294 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.42.0-1 [66.7 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.72.0-1 [300 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp1 armhf 1.7.4-3.1 [65.8 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf librhash0 armhf 1.4.0-1 [133 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libuv1 armhf 1.40.0-1 [118 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf cmake armhf 3.18.4-1+rpi1 [3113 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2.1 [188 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182-1 [162 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.3-2 [1178 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf distro-info-data all 0.45 [6668 B]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.2.0-19+rpi1 [231 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-10-dev armhf 10.2.0-19+rpi1 [278 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf gfortran-10 armhf 10.2.0-19+rpi1 [40.0 MB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:10.2.0-1+rpi1 [1428 B]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libhwloc15 armhf 2.4.0+dfsg-2 [122 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf hwloc-nox armhf 2.4.0+dfsg-2 [166 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libibverbs1 armhf 32.0-1 [52.0 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf ibverbs-providers armhf 32.0-1 [24.4 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-3 [113 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libboost1.71-dev armhf 1.71.0-7+b1 [9098 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.71.0.3+b8 [4624 B]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-1 [167 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-1 [126 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-1 [100 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-1 [56.8 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-1 [61.7 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libevent-dev armhf 2.1.12-stable-1 [281 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-double3 armhf 3.3.8-2 [429 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-single3 armhf 3.3.8-2 [633 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-bin armhf 3.3.8-2 [43.6 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-dev armhf 3.3.8-2 [1060 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libnuma1 armhf 2.0.12-1 [22.5 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf libnuma-dev armhf 2.0.12-1 [35.6 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf libltdl7 armhf 2.4.6-14 [388 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf libltdl-dev armhf 2.4.6-14 [159 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-dev armhf 2.4.0+dfsg-2 [189 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf libpciaccess0 armhf 0.16-1 [51.0 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.14-2 [135 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.12-1 [311 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.12-1 [700 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf libxnvctrl0 armhf 450.80.02-1 [25.3 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf ocl-icd-libopencl1 armhf 2.2.13-1 [36.5 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-plugins armhf 2.4.0+dfsg-2 [19.5 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf libibverbs-dev armhf 32.0-1 [179 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf node-jquery all 3.5.1+dfsg+~3.5.4-3 [396 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.4-3 [3996 B]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf libjs-jquery-ui all 1.12.1+dfsg-7 [232 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-3 [2980 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf libmpich12 armhf 3.4~a2+really3.3.2-2 [1053 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf mpich armhf 3.4~a2+really3.3.2-2 [335 kB]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf libmpich-dev armhf 3.4~a2+really3.3.2-2 [1531 kB]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf libpmix2 armhf 3.2.1-1 [369 kB]
Get:133 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi3 armhf 4.0.5-7+rpi1 [1582 kB]
Get:134 http://172.17.0.1/private bullseye-staging/main armhf openmpi-common all 4.0.5-7+rpi1 [71.4 kB]
Get:135 http://172.17.0.1/private bullseye-staging/main armhf libpmix-dev armhf 3.2.1-1 [496 kB]
Get:136 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:137 http://172.17.0.1/private bullseye-staging/main armhf openmpi-bin armhf 4.0.5-7+rpi1 [96.4 kB]
Get:138 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi-dev armhf 4.0.5-7+rpi1 [1041 kB]
Get:139 http://172.17.0.1/private bullseye-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:140 http://172.17.0.1/private bullseye-staging/main armhf xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:141 http://172.17.0.1/private bullseye-staging/main armhf x11proto-dev all 2020.1-1 [594 kB]
Get:142 http://172.17.0.1/private bullseye-staging/main armhf x11proto-core-dev all 2020.1-1 [3404 B]
Get:143 http://172.17.0.1/private bullseye-staging/main armhf libxau-dev armhf 1:1.0.8-1+b2 [22.4 kB]
Get:144 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:145 http://172.17.0.1/private bullseye-staging/main armhf xtrans-dev all 1.4.0-1 [98.7 kB]
Get:146 http://172.17.0.1/private bullseye-staging/main armhf libxcb1-dev armhf 1.14-2 [173 kB]
Get:147 http://172.17.0.1/private bullseye-staging/main armhf libx11-dev armhf 2:1.6.12-1 [781 kB]
Get:148 http://172.17.0.1/private bullseye-staging/main armhf lsb-release all 11.1.0+rpi1 [28.1 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libuchardet0:armhf.
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Setting up x11proto-core-dev (2020.1-1) ...
Setting up libevent-dev (2.1.12-stable-1) ...
Setting up liblapack-dev:armhf (3.9.0-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up gcc-10 (10.2.0-19+rpi1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13-5) ...
Setting up libnl-3-dev:armhf (3.4.0-1) ...
Setting up groff-base (1.22.4-5) ...
Setting up procps (2:3.3.16-5) ...
update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode
Setting up libcurl4:armhf (7.72.0-1) ...
Setting up libx11-6:armhf (2:1.6.12-1) ...
Setting up libgfortran-10-dev:armhf (10.2.0-19+rpi1) ...
Setting up libjs-jquery (3.5.1+dfsg+~3.5.4-3) ...
Setting up libfftw3-dev:armhf (3.3.8-2) ...
Setting up libpython3.9-stdlib:armhf (3.9.0-5+rpi1) ...
Setting up libpython3-stdlib:armhf (3.9.0-4) ...
Setting up automake (1:1.16.2-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libibverbs1:armhf (32.0-1) ...
Setting up gettext (0.19.8.1-10) ...
Setting up libstdc++-10-dev:armhf (10.2.0-19+rpi1) ...
Setting up libxcb1-dev:armhf (1.14-2) ...
Setting up g++-10 (10.2.0-19+rpi1) ...
Setting up ibverbs-providers:armhf (32.0-1) ...
Setting up mpich (3.4~a2+really3.3.2-2) ...
update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode
update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode
Setting up openssh-client (1:8.4p1-3+b1) ...
Setting up libboost1.71-dev:armhf (1.71.0-7+b1) ...
Setting up libx11-dev:armhf (2:1.6.12-1) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libxnvctrl0:armhf (450.80.02-1) ...
Setting up libnl-route-3-dev:armhf (3.4.0-1) ...
Setting up libltdl-dev:armhf (2.4.6-14) ...
Setting up libjs-jquery-ui (1.12.1+dfsg-7) ...
Setting up gfortran-10 (10.2.0-19+rpi1) ...
Setting up cmake (3.18.4-1+rpi1) ...
Setting up libhwloc-dev:armhf (2.4.0+dfsg-2) ...
Setting up libboost-dev:armhf (1.71.0.3+b8) ...
Setting up python3.9 (3.9.0-5+rpi1) ...
Setting up po-debconf (1.0.21) ...
Setting up python3 (3.9.0-4) ...
Setting up libibverbs-dev:armhf (32.0-1) ...
Setting up libhwloc-plugins:armhf (2.4.0+dfsg-2) ...
Setting up gfortran (4:10.2.0-1+rpi1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libmpich-dev:armhf (3.4~a2+really3.3.2-2) ...
update-alternatives: using /usr/include/arm-linux-gnueabihf/mpich to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up lsb-release (11.1.0+rpi1) ...
Setting up libpmix2:armhf (3.2.1-1) ...
Setting up libopenmpi3:armhf (4.0.5-7+rpi1) ...
Setting up libpmix-dev:armhf (3.2.1-1) ...
Setting up openmpi-bin (4.0.5-7+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up libopenmpi-dev:armhf (4.0.5-7+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.2.1) ...
Setting up sbuild-build-depends-gromacs-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.35.1-2+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-19+rpi1 gcc-10_10.2.0-19+rpi1 libc6-dev_2.31-4+rpi1 libstdc++-10-dev_10.2.0-19+rpi1 libstdc++6_10.2.0-19+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.11 aptitude_0.8.13-2 aptitude-common_0.8.13-2 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1~rc2-1 binutils_2.35.1-2+rpi1 binutils-arm-linux-gnueabihf_2.35.1-2+rpi1 binutils-common_2.35.1-2+rpi1 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 chrpath_0.16-2 cmake_3.18.4-1+rpi1 cmake-data_3.18.4-1+rpi1 coreutils_8.32-4 cpp_4:10.2.0-1+rpi1 cpp-10_10.2.0-19+rpi1 dash_0.5.11+git20200708+dd9ef66-2 debconf_1.5.74 debhelper_13.2.1 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 distro-info-data_0.45 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1 fdisk_2.36-3 file_1:5.38-5 findutils_4.7.0+git20201010-2 g++_4:10.2.0-1+rpi1 g++-10_10.2.0-19+rpi1 gcc_4:10.2.0-1+rpi1 gcc-10_10.2.0-19+rpi1 gcc-10-base_10.2.0-19+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gfortran_4:10.2.0-1+rpi1 gfortran-10_10.2.0-19+rpi1 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 hwloc-nox_2.4.0+dfsg-2 ibverbs-providers_32.0-1 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 krb5-locales_1.17-10 libacl1_2.2.53-8 libapt-pkg6.0_2.1.11 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libasan6_10.2.0-19+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-19+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3.1 libaudit1_1:2.8.5-3.1 libbinutils_2.35.1-2+rpi1 libblas-dev_3.9.0-3 libblas3_3.9.0-3 libblkid1_2.36-3 libboost-dev_1.71.0.3+b8 libboost-iostreams1.71.0_1.71.0-7 libboost1.71-dev_1.71.0-7+b1 libbrotli1_1.0.9-2+b1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-4 libc-bin_2.31-4+rpi1 libc-dev-bin_2.31-4+rpi1 libc6_2.31-4+rpi1 libc6-dev_2.31-4+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcbor0_0.5.0+dfsg-2 libcc1-0_10.2.0-19+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-2+rpi1 libctf0_2.35.1-2+rpi1 libcurl4_7.72.0-1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.255 libdebhelper-perl_13.2.1 libdpkg-perl_1.20.5+rpi1 libedit2_3.1-20191231-1 libelf1_0.182-1 libevent-2.1-7_2.1.12-stable-1 libevent-core-2.1-7_2.1.12-stable-1 libevent-dev_2.1.12-stable-1 libevent-extra-2.1-7_2.1.12-stable-1 libevent-openssl-2.1-7_2.1.12-stable-1 libevent-pthreads-2.1-7_2.1.12-stable-1 libexpat1_2.2.10-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1 libfdisk1_2.36-3 libffi7_3.3-5 libfftw3-bin_3.3.8-2 libfftw3-dev_3.3.8-2 libfftw3-double3_3.3.8-2 libfftw3-single3_3.3.8-2 libfido2-1_1.5.0-2 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-19+rpi1 libgcc-s1_10.2.0-19+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libgfortran-10-dev_10.2.0-19+rpi1 libgfortran5_10.2.0-19+rpi1 libglib2.0-0_2.66.3-2 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.15-4 libgomp1_10.2.0-19+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10+b3 libhogweed6_3.6-2 libhwloc-dev_2.4.0+dfsg-2 libhwloc-plugins_2.4.0+dfsg-2 libhwloc15_2.4.0+dfsg-2 libibverbs-dev_32.0-1 libibverbs1_32.0-1 libicu67_67.1-4 libidn2-0_2.3.0-3 libisl22_0.22.1-1 libisl23_0.23-1 libjs-jquery_3.5.1+dfsg+~3.5.4-3 libjs-jquery-ui_1.12.1+dfsg-7 libjsoncpp1_1.7.4-3.1 libk5crypto3_1.17-10+b3 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10+b3 libkrb5support0_1.17-10+b3 libksba8_1.4.0-2 liblapack-dev_3.9.0-3 liblapack3_3.9.0-3 libldap-2.4-2_2.4.56+dfsg-1+rpi1 libldap-common_2.4.56+dfsg-1+rpi1 libltdl-dev_2.4.6-14 libltdl7_2.4.6-14 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-3 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libmpich-dev_3.4~a2+really3.3.2-2 libmpich12_3.4~a2+really3.3.2-2 libncurses6_6.2+20201114-1 libncursesw6_6.2+20201114-1 libnettle8_3.6-2 libnghttp2-14_1.42.0-1 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libnuma-dev_2.0.12-1 libnuma1_2.0.12-1 libopenmpi-dev_4.0.5-7+rpi1 libopenmpi3_4.0.5-7+rpi1 libp11-kit0_0.23.21-2 libpam-cap_1:2.44-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpciaccess0_0.16-1 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.32_5.32.0-5 libpipeline1_1.5.3-1 libpmix-dev_3.2.1-1 libpmix2_3.2.1-1 libprocps8_2:3.3.16-5 libpsl5_0.21.0-1.1 libpthread-stubs0-dev_0.4-1 libpython3-stdlib_3.9.0-4 libpython3.9-minimal_3.9.0-5+rpi1 libpython3.9-stdlib_3.9.0-5+rpi1 libreadline8_8.1~rc2-2 librhash0_1.4.0-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.0-3+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.4-2 libsigsegv2_2.12-2 libsmartcols1_2.36-3 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1h-1 libstdc++-10-dev_10.2.0-19+rpi1 libstdc++6_10.2.0-19+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.6-2+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-14 libubsan1_10.2.0-19+rpi1 libuchardet0_0.0.7-1 libudev1_246.6-2+rpi1 libunistring2_0.9.10-4 libuuid1_2.36-3 libuv1_1.40.0-1 libx11-6_2:1.6.12-1 libx11-data_2:1.6.12-1 libx11-dev_2:1.6.12-1 libxapian30_1.4.17-1 libxau-dev_1:1.0.8-1+b2 libxau6_1:1.0.8-1+b2 libxcb1_1.14-2 libxcb1-dev_1.14-2 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxml2_2.9.10+dfsg-6.3 libxnvctrl0_450.80.02-1 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 lsb-release_11.1.0+rpi1 m4_1.4.18-4 mailcap_3.67 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 media-types_1.0.1 mime-support_3.66 mount_2.36-3 mpich_3.4~a2+really3.3.2-2 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 netbase_6.2 node-jquery_3.5.1+dfsg+~3.5.4-3 ocl-icd-libopencl1_2.2.13-1 openmpi-bin_4.0.5-7+rpi1 openmpi-common_4.0.5-7+rpi1 openssh-client_1:8.4p1-3+b1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.32.0-5 perl-base_5.32.0-5 perl-modules-5.32_5.32.0-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21 procps_2:3.3.16-5 python3_3.9.0-4 python3-minimal_3.9.0-4 python3.9_3.9.0-5+rpi1 python3.9-minimal_3.9.0-5+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1~rc2-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gromacs-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-5 tar_1.30+dfsg-7 tzdata_2020d-1 util-linux_2.36-3 x11proto-core-dev_2020.1-1 x11proto-dev_2020.1-1 xorg-sgml-doctools_1:1.11-1 xtrans-dev_1.4.0-1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.R_AW4uyi/trustedkeys.kbx': General error
gpgv: Signature made Thu Oct 22 02:13:15 2020 UTC
gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F
gpgv: issuer "nbreen@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./gromacs_2020.4-2.dsc
dpkg-source: info: extracting gromacs in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking gromacs_2020.4.orig.tar.gz
dpkg-source: info: unpacking gromacs_2020.4-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying disable-listed-forces-test.patch
dpkg-source: info: applying arm64-disable-numa-test.patch
dpkg-source: info: applying readme.patch
dpkg-source: info: applying copyright-file.patch
dpkg-source: info: applying disable-cpuinfotest.patch
dpkg-source: info: applying mdrun-test-timeout.patch
dpkg-source: info: applying local-mathjax.patch
dpkg-source: info: applying mpi-tests-localhost.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-abc2f364-3fce-46c3-91d6-61f9973e38ed
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package gromacs
dpkg-buildpackage: info: source version 2020.4-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh_testdir
dh_testroot
rm -rf build docs/doxygen/*.pyc
dh_clean build-basic build-mpich build-openmpi build-manual configure-stamp \
debian/gromacs-mpich.README.Debian debian/gromacs-openmpi.README.Debian
debian/rules binary-arch
dh_testdir
(mkdir -p build/basic; cd build/basic; cmake /<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_INSTALL_LEGACY_API=ON)
-- The C compiler identification is GNU 10.2.0
-- The CXX compiler identification is GNU 10.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.0", minimum required is "1.5")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Using dynamic plugins (e.g VMD-supported file formats)
-- Checking for suitable VMD version
-- VMD plugins not found. Path to VMD can be set with VMDDIR.
-- Using default binary suffix: ""
-- Using default library suffix: ""
-- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized
Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pygments'
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1")
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Doxygen not found. Documentation targets will not be generated.
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic
(mkdir -p build/basic-dp; cd build/basic-dp; cmake /<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_DOUBLE=ON)
-- The C compiler identification is GNU 10.2.0
-- The CXX compiler identification is GNU 10.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:217 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.0", minimum required is "1.5")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Using dynamic plugins (e.g VMD-supported file formats)
-- Checking for suitable VMD version
-- VMD plugins not found. Path to VMD can be set with VMDDIR.
-- Using default binary suffix: "_d"
-- Using default library suffix: "_d"
-- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized
Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pygments'
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1")
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Doxygen not found. Documentation targets will not be generated.
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic-dp
(mkdir -p build/mpich; cd build/mpich; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.mpich" -DGMX_LIBS_SUFFIX="_mpi.mpich")
-- The C compiler identification is GNU 10.2.0
-- The CXX compiler identification is GNU 10.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/mpicc.mpich - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi.mpich"
-- Using manually set library suffix: "_mpi.mpich"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpich
(mkdir -p build/mpich-dp; cd build/mpich-dp; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.mpich" -DGMX_LIBS_SUFFIX="_mpi_d.mpich")
-- The C compiler identification is GNU 10.2.0
-- The CXX compiler identification is GNU 10.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/mpicc.mpich - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:217 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi_d.mpich"
-- Using manually set library suffix: "_mpi_d.mpich"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpich-dp
(mkdir -p build/openmpi; cd build/openmpi; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.openmpi" -DGMX_LIBS_SUFFIX="_mpi.openmpi")
-- The C compiler identification is GNU 10.2.0
-- The CXX compiler identification is GNU 10.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/mpicc.openmpi - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi.openmpi"
-- Using manually set library suffix: "_mpi.openmpi"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/openmpi
(mkdir -p build/openmpi-dp; cd build/openmpi-dp; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.4-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.openmpi" -DGMX_LIBS_SUFFIX="_mpi_d.openmpi")
-- The C compiler identification is GNU 10.2.0
-- The CXX compiler identification is GNU 10.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/mpicc.openmpi - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:217 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv8 Processor rev 1 (v8l)
-- Detected build CPU family - 8
-- Detected build CPU model - 0
-- Detected build CPU stepping - 1
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
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-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
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-- Looking for cheev_
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-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi_d.openmpi"
-- Using manually set library suffix: "_mpi_d.openmpi"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
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-- Performing Test HAS_NO_UNUSED_PARAMETER
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-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/openmpi-dp
touch configure-stamp
dh_testdir
/usr/bin/make -j4 -C build/basic
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/alltoall.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_protocol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/barrier.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_send_recv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/bcast.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_wait.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/collective.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/profile.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/comm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 0%] Built target lmfit_objlib
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/event.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce_fast.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/gather.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scatter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/group.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_init.cpp
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
Scanning dependencies of target linearalgebra
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/list.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/type.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 1%] Built target scanner
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scan.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/3dview.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/buttons.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/dialogs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/fgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/filter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/logo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/molps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 6%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/pulldown.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
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/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
2280 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:457:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
457 | calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:481:42: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
481 | calcUmbrellaForceAndPotential(dimParams, grid, coordState_.umbrellaGridpoint(), newForce);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
242 | newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/anadih.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/angle_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/binsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/cmat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dens_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dlist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/eigio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/fitahx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_anaeig.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_analyze.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bundle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_chi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_confrms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_covar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_current.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_density.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densmap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densorder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dielectric.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dipoles.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_disre.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_mapping&}; _Tp = t_mapping; _Alloc = std::allocator<t_mapping>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_mapping>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void prune_ss_legend(t_matrix*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dos.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dyecoupl.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_velacc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wham.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wheel.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/hxprops.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nrama.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void rainbow_map(gmx_bool, gmx::ArrayRef<t_mapping>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1328:13: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1328 | static void rainbow_map(gmx_bool bBlue, gmx::ArrayRef<t_mapping> map)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void leg_continuous(t_psdata*, real, real, real, const string&, real, char*, gmx::ArrayRef<const t_mapping>, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:249:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
249 | static void leg_continuous(t_psdata* ps,
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nsfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/powerspect.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void ps_mat(const char*, gmx::ArrayRef<t_matrix>, gmx::ArrayRef<t_matrix>, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, int, real, real, real, const char*, const char*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
1033 | leg_continuous(&out, x0 + w / 2, w / 2, DDD, legend, psr->legfontsize, psr->legfont,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1034 | leg_map, mapoffset);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
316 | leg_continuous(ps, xx1, x1, y0, label1, fontsize, font, map1, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
317 | leg_continuous(ps, xx2, x2, y0, label2, fontsize, font, map2, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/pp2shift.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'int gmx_xpm2ps(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/princ.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/sfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/calch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/fflibutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genconf.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setvelocities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/topologyinformation.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp: In member function 'void gmx::UpdateConstrainCuda::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
70 | void UpdateConstrainCuda::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<float> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_testutils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1280:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1280 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1281 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1282 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1283 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<float> >, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:114:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
114 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/vmdio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/legacymodules.cpp.o -c /<<PKGBUILDDIR>>/src/programs/legacymodules.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/context.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/context.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/gmxapi.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/gmxapi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx ../../lib/libgromacs.so.5.0.0 /usr/lib/arm-linux-gnueabihf/libX11.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/md.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/md.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdsignals.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdsignals.cpp
cd /<<PKGBUILDDIR>>/build/basic/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/template.dir/template.cpp.o -o ../../bin/template ../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
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cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/session.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/session.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/status.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/system.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/version.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/tpr.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi.so.0 -o ../../../lib/libgmxapi.so.0.1.0 CMakeFiles/gmxapi.dir/context.cpp.o CMakeFiles/gmxapi.dir/exceptions.cpp.o CMakeFiles/gmxapi.dir/gmxapi.cpp.o CMakeFiles/gmxapi.dir/md.cpp.o CMakeFiles/gmxapi.dir/mdmodule.cpp.o CMakeFiles/gmxapi.dir/mdsignals.cpp.o CMakeFiles/gmxapi.dir/session.cpp.o CMakeFiles/gmxapi.dir/status.cpp.o CMakeFiles/gmxapi.dir/system.cpp.o CMakeFiles/gmxapi.dir/version.cpp.o CMakeFiles/gmxapi.dir/workflow.cpp.o CMakeFiles/gmxapi.dir/tpr.cpp.o ../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libgmxapi.so.0.1.0 ../../../lib/libgmxapi.so.0 ../../../lib/libgmxapi.so
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/alltoall.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_protocol.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
Scanning dependencies of target linearalgebra
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/barrier.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_send_recv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/bcast.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_wait.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/collective.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/profile.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/comm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/event.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce_fast.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/gather.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scatter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/group.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_init.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/list.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/type.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 1%] Built target linearalgebra
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scan.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
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[ 4%] Built target thread_mpi
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/vmddlopen.dir/__/__/external/vmd_molfile/vmddlopen.cpp.o -c /<<PKGBUILDDIR>>/src/external/vmd_molfile/vmddlopen.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 4%] Built target vmddlopen
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp: In member function 'void gmx::CheckpointHelper::writeCheckpoint(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp:129:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
129 | mdoutf_write_to_trajectory_files(fplog_, cr_, trajectoryElement_->outf_, MDOF_CPT,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
130 | globalNumAtoms_, step, time, localStateInstance_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
131 | state_global_, observablesHistory_, ArrayRef<RVec>());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 4%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp: In member function 'void gmx::EnergyElement::doStep(gmx::Time, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | sum_dhdl(enerd_, freeEnergyPerturbationElement_->constLambdaView(), *inputrec_->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp: In member function 'void gmx::ForceElement::run(gmx::Step, gmx::Time, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp:159:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
159 | do_force(fplog_, cr_, ms, inputrec_, awh, enforcedRotation_, imdSession_, pull_work_, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
160 | nrnb_, wcycle_, localTopology_, box, x, hist, forces, force_vir, mdAtoms_->mdatoms(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
161 | energyElement_->enerdata(), fcd_, lambda, graph, fr_, runScheduleWork_, vsite_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
162 | energyElement_->muTot(), time, ed, static_cast<int>(flags), ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target view_objlib
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/3dview.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In member function 'void gmx::FreeEnergyPerturbationElement::updateLambdas(gmx::Step)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:86:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
86 | setCurrentLambdasLocal(step, inputrec_->fepvals, lambda0_.data(), lambda_, currentFEPState_);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In constructor 'gmx::FreeEnergyPerturbationElement::FreeEnergyPerturbationElement(FILE*, const t_inputrec*, gmx::MDAtoms*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:68:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
68 | initialize_lambdas(fplog_, *inputrec_, true, ¤tFEPState_, lambda_, lambda0_.data());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/buttons.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/dialogs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/fgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp: In constructor 'gmx::ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int, int, real, gmx::Step, gmx::ArrayRef<double [3]>, gmx::PropagatorCallbackPtr, gmx::StatePropagatorData*, gmx::EnergyElement*, FILE*, const t_inputrec*, const gmx::MDAtoms*, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:62:1: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
62 | ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int nstpcouple,
| ^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/logo.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp: In member function 'void gmx::PmeLoadBalanceHelper::run(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp:107:19: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
107 | pme_loadbal_do(pme_loadbal_, cr_, (isVerbose_ && MASTER(cr_)) ? stderr : nullptr, fplog_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
108 | mdlog_, *inputrec_, fr_, statePropagatorData_->constBox(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
109 | statePropagatorData_->constPositionsView().paddedArrayRef(), wcycle_, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
110 | step - inputrec_->init_step, &bPMETunePrinting_, false);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/manager.cpp
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp: In function 'bool ManCallBack(t_x11*, XEvent*, Window, void*)':
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:366:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
366 | put_atoms_in_compact_unitcell(man->molw->ePBC, ecenterDEF, man->box, atomsArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:366:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/molps.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 6%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp: In member function 'void gmx::ShellFCElement::run(gmx::Step, gmx::Time, bool, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp:185:24: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
185 | relax_shell_flexcon(fplog_, cr_, ms, isVerbose_, enforcedRotation_, step, inputrec_, imdSession_,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
186 | pull_work_, isNSStep, static_cast<int>(flags), localTopology_, constr_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
187 | energyElement_->enerdata(), fcd_, statePropagatorData_->localNumAtoms(), x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
188 | v, box, lambda, hist, forces, force_vir, mdAtoms_->mdatoms(), nrnb_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
189 | wcycle_, graph, shellfc_, fr_, runScheduleWork_, time,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
190 | energyElement_->muTot(), vsite_, ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/pulldown.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/isimulator.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp:44:
/usr/include/c++/10/bits/unique_ptr.h: In member function 'std::unique_ptr<gmx::ISimulatorElement> gmx::ModularSimulator::buildIntegrator(gmx::SignallerBuilder<gmx::NeighborSearchSignaller>*, gmx::SignallerBuilder<gmx::EnergySignaller>*, gmx::SignallerBuilder<gmx::LoggingSignaller>*, gmx::TrajectoryElementBuilder*, std::vector<gmx::ICheckpointHelperClient*>*, gmx::CheckBondedInteractionsCallbackPtr*, gmx::compat::not_null<gmx::StatePropagatorData*>, gmx::compat::not_null<gmx::EnergyElement*>, gmx::FreeEnergyPerturbationElement*, bool)':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 9%] Built target view_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::_ZN3gmx19StatePropagatorData24trajectoryWriterTeardownEP10gmx_mdoutf.part.0(gmx_mdoutf*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:464:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
464 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:466:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
466 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp: In constructor 'gmx::VRescaleThermostat::VRescaleThermostat(int, int, bool, int64_t, int, double, const real*, const real*, const real*, gmx::EnergyElement*, gmx::ArrayRef<double>, gmx::PropagatorCallbackPtr, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp:59:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
59 | VRescaleThermostat::VRescaleThermostat(int nstcouple,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::write(gmx_mdoutf_t, gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:411:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
411 | mdoutf_write_to_trajectory_files(fplog_, cr_, outf, static_cast<int>(mdof_flags),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
412 | totalNumAtoms_, currentStep, currentTime,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
413 | localStateBackup_.get(), globalState_, observablesHistory, f_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::StatePropagatorData::setLocalState(std::unique_ptr<t_state>)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::StatePropagatorData::StatePropagatorData(int, FILE*, const t_commrec*, t_state*, int, int, int, int, bool, gmx::FreeEnergyPerturbationElement*, const gmx::TopologyHolder*, bool, bool, std::string, const t_inputrec*, const t_mdatoms*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 10%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp: In function 'void Nbnxm::setupAndRunInstance(const gmx::BenchmarkSystem&, const Nbnxm::KernelBenchOptions&, bool)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:222:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
222 | nbnxn_put_on_grid(nbv.get(), system.box, 0, lowerCorner, upperCorner, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
223 | { 0, int(system.coordinates.size()) }, atomDensity, atomInfo,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | system.coordinates, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function 'void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:1484:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1484 | void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t& nbat, gmx::ArrayRef<gmx::RVec> fshift)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Nbnxm::KernelBenchOptions&}; _Tp = Nbnxm::KernelBenchOptions; _Alloc = std::allocator<Nbnxm::KernelBenchOptions>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Nbnxm::KernelBenchOptions>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In function 'void Nbnxm::bench(int, const Nbnxm::KernelBenchOptions&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In function '_ZN5Nbnxm7GridSet9putOnGridEPA3_KdiPS1_S4_PKN3gmx15UpdateGroupsCogENS5_5RangeIiEEdNS5_8ArrayRefIKiEENSB_IKNS5_11BasicVectorIdEEEEiPSC_P16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:216:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
216 | Grid::calcColumnIndices(grid.dimensions(), updateGroupsCog, atomRange, x, ddZone, move, thread,
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
217 | nthread, gridSetData_.cells, gridWork_[thread].numAtomsPerColumn);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::fillCell(Nbnxm::GridSetData*, nbnxn_atomdata_t*, int, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, Nbnxm::BoundingBox*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:859:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
859 | void Grid::fillCell(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In member function 'void Nbnxm::GridSet::putOnGrid(const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:136:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
136 | void GridSet::putOnGrid(const matrix box,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:223:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
223 | grid.setCellIndices(ddZone, cellOffset, &gridSetData_, gridWork_, atomRange, atomInfo.data(), x,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | numAtomsMoved, nbat);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsCpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:987:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
987 | void Grid::sortColumnsCpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1027:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1027 | fillCell(gridSetData, nbat, atomOffsetCell, atomOffsetCell + numAtomsCell, atinfo, x, nullptr);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsGpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1050:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1050 | void Grid::sortColumnsGpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1151:29: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1151 | fillCell(gridSetData, nbat, atomOffsetX, atomOffsetX + numAtomsX, atinfo, x,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1152 | bb_work_aligned);
| ~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In function '_ZN5Nbnxm4Grid14setCellIndicesEiiPNS_11GridSetDataEN3gmx8ArrayRefINS_8GridWorkEEENS3_5RangeIiEEPKiNS4_IKNS3_11BasicVectorIdEEEEiP16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1409:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1409 | sortColumnsGpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1410 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1404:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1404 | sortColumnsCpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1405 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In static member function 'static void Nbnxm::Grid::calcColumnIndices(const Nbnxm::Grid::Dimensions&, const gmx::UpdateGroupsCog*, gmx::Range<int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, int, int, gmx::ArrayRef<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1172:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1172 | void Grid::calcColumnIndices(const Grid::Dimensions& gridDims,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::setCellIndices(int, int, Nbnxm::GridSetData*, gmx::ArrayRef<Nbnxm::GridWork>, gmx::Range<int>, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1286 | void Grid::setCellIndices(int ddZone,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp: In member function 'void nonbonded_verlet_t::dispatchNonbondedKernel(gmx::InteractionLocality, const interaction_const_t&, const gmx::StepWorkload&, int, const t_forcerec&, gmx_enerdata_t*, t_nrnb*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp:442:33: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
442 | nbnxn_kernel_gpu_ref(
| ~~~~~~~~~~~~~~~~~~~~^
443 | pairlistSet.gpuList(), nbat.get(), &ic, fr.shift_vec, stepWork, clearF,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
444 | nbat->out[0].f, nbat->out[0].fshift.data(), enerd->grpp.ener[egCOULSR].data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
445 | fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp: In function 'void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu*, const nbnxn_atomdata_t*, const interaction_const_t*, real (*)[3], const gmx::StepWorkload&, int, gmx::ArrayRef<double>, real*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
57 | void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu* nbl,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid(nonbonded_verlet_t*, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
57 | void nbnxn_put_on_grid(nonbonded_verlet_t* nb_verlet,
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:53:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.h:184:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
184 | gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
185 | atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*, const gmx_domdec_zones_t*, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:76:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
76 | void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t* nbv,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:90:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
90 | nbnxn_put_on_grid(nbv, nullptr, zone, c0, c1, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
91 | { zones->cg_range[zone], zones->cg_range[zone + 1] }, -1, atomInfo, x, 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
92 | nullptr);
| ~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::convertCoordinates(gmx::AtomLocality, bool, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
126 | void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(gmx::AtomLocality, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:159:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
159 | void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::PinningPolicy}; _Tp = NbnxnPairlistGpu; _Alloc = std::allocator<NbnxnPairlistGpu>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<NbnxnPairlistGpu>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
/usr/include/c++/10/bits/vector.tcc: In constructor 'PairlistSet::PairlistSet(gmx::InteractionLocality, const PairlistParams&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, tmpi_comm_* const*, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:232:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
232 | static void low_set_ddbox(int numPbcDimensions,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:278:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
278 | void set_ddbox(const gmx_domdec_t& dd,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
291 | low_set_ddbox(dd.unitCellInfo.npbcdim, dd.unitCellInfo.numBoundedDimensions, &dd.nc, box,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
292 | calculateUnboundedSize, xRef,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr, ddbox);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(const t_commrec&, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:302:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
302 | void set_ddbox_cr(const t_commrec& cr,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:311:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
311 | low_set_ddbox(ePBC2npbcdim(ir.ePBC), inputrec2nboundeddim(&ir), dd_nc, box, true, x, nullptr, ddbox);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, const t_state*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
228 | void dd_collect_vec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:291:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
291 | dd_collect_vec(dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:296:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
296 | dd_collect_vec(dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:301:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
301 | dd_collect_vec(dd, state_local, state_local->cg_p, globalCgpRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp: In function 'void distributeVec(gmx_domdec_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:143:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
143 | static void distributeVec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:143:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp: In function 'void distributeState(const gmx::MDLogger&, gmx_domdec_t*, const gmx_mtop_t&, t_state*, const gmx_ddbox_t&, t_state*, PaddedHostVector<gmx::BasicVector<double> >*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:259:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
259 | distributeVec(dd, DDMASTER(dd) ? state->x : gmx::ArrayRef<const gmx::RVec>(), state_local->x);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:259:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:259:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:263:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
263 | distributeVec(dd, DDMASTER(dd) ? state->v : gmx::ArrayRef<const gmx::RVec>(), state_local->v);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:263:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:263:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:267:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
267 | distributeVec(dd, DDMASTER(dd) ? state->cg_p : gmx::ArrayRef<const gmx::RVec>(), state_local->cg_p);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:267:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:267:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
118 | void ddSendrecv(const gmx_domdec_t* dd,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3156:17: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3156 | static gmx_bool test_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3166:14: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3166 | set_ddbox(*dd, false, box, true, x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool change_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3228:10: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3228 | gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp: In function 'DDGridSetup getDDGridSetup(const gmx::MDLogger&, const t_commrec*, int, const gmx::DomdecOptions&, const DDSettings&, const DDSystemInfo&, real, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:906:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
906 | DDGridSetup getDDGridSetup(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:934:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
934 | set_ddbox_cr(*cr, &numDomainsLegacyIvec, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:938:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
938 | set_ddbox_cr(*cr, nullptr, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::Impl::Impl(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3045:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3045 | DomainDecompositionBuilder::Impl::Impl(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2967:82: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2967 | gridSetupCellsizeLimit, mtop, ir, box, xGlobal, &ddbox);
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3091:92: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3091 | gridSetupCellsizeLimit, mtop_, ir_, box, xGlobal, &ddbox_);
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::DomainDecompositionBuilder(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3134:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3134 | DomainDecompositionBuilder::DomainDecompositionBuilder(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3143:95: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3143 | impl_(new Impl(mdlog, cr, options, mdrunOptions, prefer1DAnd1Pulse, mtop, ir, box, xGlobal))
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
531 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
595 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:272:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
272 | void dd_move_x(gmx_domdec_t* dd, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_wallcycle* wcycle)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
349 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ForceWithShiftForces*, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
424 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void dd_resize_state(t_state*, PaddedHostVector<gmx::BasicVector<double> >*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
253 | ddSendrecv(dd, d, dddirBackward, gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
254 | gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::scale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:65:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
65 | void ScaleCoordinates::Impl::scale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:75:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
75 | void ScaleCoordinates::Impl::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
97 | void ScaleCoordinates::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:99:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
99 | impl_->scale(coordinates);
| ~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:102:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
102 | void ScaleCoordinates::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:102:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:104:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
104 | impl_->inverseIgnoringZeroScale(coordinates);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::Impl::transform(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:140:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
140 | void TranslateAndScale::Impl::transform(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:161:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
161 | void TranslateAndScale::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:163:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
163 | impl_->transform(coordinates);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2104 | ddSendrecv<gmx::RVec>(dd, dim_ind, dddirBackward, work.positionBuffer, rvecBufferRef);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t&, const t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx_vsite_t*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2866:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2866 | set_ddbox(*dd, true, DDMASTER(dd) ? state_global->box : nullptr, true, xGlobal, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2907:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2907 | set_ddbox(*dd, bMasterState, state_local->box, true, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2928:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2928 | set_ddbox(*dd, bMasterState, state_local->box, bNStGlobalComm, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2946 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2947 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), state_local->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2970 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2971 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2972 | state_local->x);
| ~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3005:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3005 | nbnxn_put_on_grid(fr->nbv.get(), state_local->box, 0, comm->zones.size[0].bb_x0,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3006 | comm->zones.size[0].bb_x1, comm->updateGroupsCog.get(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3007 | { 0, dd->ncg_home }, comm->zones.dens_zone0, fr->cginfo, state_local->x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3008 | ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::index))[3]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:208:7: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
208 | rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n)
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'void initialize_lambdas(FILE*, const t_inputrec&, bool, int*, gmx::ArrayRef<double>, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:282:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
282 | void initialize_lambdas(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1394:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1394 | void put_atoms_in_box(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box_omp(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1454:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1454 | void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_unused int nth)
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1470:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1470 | void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(int, int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1527 | void put_atoms_in_compact_unitcell(int ePBC, int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_molecule_com_in_box(int, int, t_block*, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
289 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_residue_com_in_box(int, int, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
341 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp:53:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BaseEntry}; _Tp = BaseEntry; _Alloc = std::allocator<BaseEntry>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BaseEntry>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void readProperty(AtomProperty*, ResidueType*, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BaseEntry*, std::vector<BaseEntry> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp:52:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator<swap_group>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<swap_group>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 't_swap* init_swapcoords(FILE*, const t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const gmx::MdrunOptions&, gmx::StartingBehavior)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp:48:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator<edpar>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::unique_ptr<gmx::EssentialDynamics> ed_open(int, ObservablesHistory*, const char*, const char*, gmx::StartingBehavior, const gmx_output_env_t*, const t_commrec*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
2280 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef<const gmx::BasicVector<double> >, const t_pbc&, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
949 | bool pullCheckPbcWithinGroup(const pull_t& pull,
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:457:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
457 | calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:481:42: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
481 | calcUmbrellaForceAndPotential(dimParams, grid, coordState_.umbrellaGridpoint(), newForce);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
242 | newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/anadih.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/angle_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/binsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/cmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dens_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dlist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/eigio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/fitahx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_anaeig.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_analyze.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bar.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:54:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'int gmx_awh(int, char**)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bundle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_chi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_confrms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_covar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_current.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_density.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densmap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dielectric.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dipoles.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_disre.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_mapping&}; _Tp = t_mapping; _Alloc = std::allocator<t_mapping>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_mapping>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'int strip_dssp(FILE*, int, const gmx_bool*, real, real*, FILE*, t_matrix*, int*, const gmx_output_env_t*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In function 'void prune_ss_legend(t_matrix*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dos.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dyecoupl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_enemat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_gyrate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_h2order.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hbond.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helixorient.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hydorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_lie.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_make_edi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mdmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmeig.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In constructor 't_corr::t_corr(int, int, int, real, int, gmx_bool, gmx_bool, real, const t_topology*, real, real)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmens.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_order.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'int gmx_nmtraj(int, char**)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp:44:
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_polystat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_potential.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_principal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rama.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotacf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saltbr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sans.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saxs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sham.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sigeps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sorient.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spatial.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_tcaf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_vanhove.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::BenchmarkSystem::BenchmarkSystem(int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_velacc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wham.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wheel.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/hxprops.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nrama.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void rainbow_map(gmx_bool, gmx::ArrayRef<t_mapping>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1328:13: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1328 | static void rainbow_map(gmx_bool bBlue, gmx::ArrayRef<t_mapping> map)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void leg_continuous(t_psdata*, real, real, real, const string&, real, char*, gmx::ArrayRef<const t_mapping>, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:249:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
249 | static void leg_continuous(t_psdata* ps,
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nsfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/powerspect.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void ps_mat(const char*, gmx::ArrayRef<t_matrix>, gmx::ArrayRef<t_matrix>, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, int, real, real, real, const char*, const char*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
1033 | leg_continuous(&out, x0 + w / 2, w / 2, DDD, legend, psr->legfontsize, psr->legfont,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1034 | leg_map, mapoffset);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
316 | leg_continuous(ps, xx1, x1, y0, label1, fontsize, font, map1, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
317 | leg_continuous(ps, xx2, x2, y0, label2, fontsize, font, map2, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/pp2shift.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'int gmx_xpm2ps(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/princ.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/sfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcZeroPointEnergy(gmx::ArrayRef<const double>, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:53:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
53 | double calcZeroPointEnergy(gmx::ArrayRef<const real> eigval, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalInternalEnergy(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:66:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
66 | double calcVibrationalInternalEnergy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalHeatCapacity(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:93:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
93 | double calcVibrationalHeatCapacity(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcQuasiHarmonicEntropy(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:158:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
158 | double calcQuasiHarmonicEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool bLinear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcSchlitterEntropy(gmx::ArrayRef<const double>, real, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:185:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
185 | double calcSchlitterEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool bLinear)
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/calch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/editconf.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_param(InteractionsOfType*, int, int, gmx::ArrayRef<const double>, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:55:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
55 | void add_param(InteractionsOfType* ps, int ai, int aj, gmx::ArrayRef<const real> c, const char* s)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:64:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
64 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm, s ? s : ""));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:64:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite4_atoms(InteractionsOfType*, int, int, int, int, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:101:66: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
101 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:101:66: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/fflibutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite3_atoms(InteractionsOfType*, int, int, int, int, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:90:66: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
90 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:90:66: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_cmap_param(InteractionsOfType*, int, int, int, int, int, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:70:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
70 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}, s ? s : ""));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:70:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite2_param(InteractionsOfType*, int, int, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:77:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
77 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:77:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite3_param(InteractionsOfType*, int, int, int, int, real, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:84:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
84 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:84:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void enter_function(const InteractionsOfType*, t_functype, int, real, gmx_ffparams_t*, InteractionList*, bool, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void enter_function(const InteractionsOfType*, t_functype, int, real, gmx_ffparams_t*, InteractionList*, bool, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<InteractionOfType, int>}; _Tp = std::pair<InteractionOfType, int>; _Alloc = std::allocator<std::pair<InteractionOfType, int> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<InteractionOfType, int> >::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp: In function 'std::vector<InteractionOfType> clean_dih(gmx::ArrayRef<const InteractionOfType>, gmx::ArrayRef<const InteractionOfType>, t_atoms*, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:252:39: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
252 | static std::vector<InteractionOfType> clean_dih(gmx::ArrayRef<const InteractionOfType> dih,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:252:39: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<InteractionOfType, int>*, std::vector<std::pair<InteractionOfType, int> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<InteractionOfType, int>*, std::vector<std::pair<InteractionOfType, int> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1881 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_6ring(t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, real, real, real, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Distance = int; _Tp = InteractionOfType; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/10/bits/stl_heap.h:424:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
424 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1666:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1666 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MoleculePatch&}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_his(t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function 'void expand_hackblocks_one(const MoleculePatchDatabase&, std::string, std::vector<MoleculePatch>*, bool, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp: In function 'void gen_pad(t_atoms*, gmx::ArrayRef<const PreprocessResidue>, gmx::ArrayRef<InteractionsOfType>, t_excls*, gmx::ArrayRef<MoleculePatchDatabase>, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:674:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
674 | ang.push_back(InteractionOfType(atomNumbers, {}, name));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:674:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:725:102: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
725 | dih.push_back(InteractionOfType(atomNumbers, {}, name));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:725:102: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:735:82: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
735 | dih.push_back(InteractionOfType(atoms, {}, ""));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:735:82: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:754:90: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
754 | pai.push_back(InteractionOfType(atoms, {}, ""));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:754:90: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:809:79: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
809 | ang.push_back(InteractionOfType(atomNumbers, {}, bondeds.s));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:809:79: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:847:79: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
847 | dih.push_back(InteractionOfType(atomNumbers, {}, bondeds.s));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:847:79: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:889:65: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
889 | rtpFFDB[0].bRemoveDihedralIfWithImproper);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:889:65: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:889:65: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:389:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
389 | improper.emplace_back(InteractionOfType(ai, {}, bondeds.s));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:389:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genion.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_trp(PreprocessingAtomTypes*, std::vector<gmx::BasicVector<double> >*, t_atom**, char****, int**, int**, int**, t_symtab*, int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int**, t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, int, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_tyr(PreprocessingAtomTypes*, std::vector<gmx::BasicVector<double> >*, t_atom**, char****, int**, int**, int**, t_symtab*, int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int**, t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, int, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genrestr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gmxcpp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'void do_vsites(gmx::ArrayRef<const PreprocessResidue>, PreprocessingAtomTypes*, t_atoms*, t_symtab*, std::vector<gmx::BasicVector<double> >*, gmx::ArrayRef<InteractionsOfType>, int**, int**, real, bool, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:2247:101: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2247 | *parm = InteractionOfType(newAtomNumber, parm->forceParam(), parm->interactionTypeName());
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:2247:101: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&, char**, const InteractionOfType&, int&, int&}; _Tp = AtomTypeData; _Alloc = std::allocator<AtomTypeData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AtomTypeData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'int PreprocessingAtomTypes::addType(t_symtab*, const t_atom&, const string&, const InteractionOfType&, int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/c++/10/bits/c++allocator.h:33,
from /usr/include/c++/10/bits/allocator.h:46,
from /usr/include/c++/10/string:41,
from /usr/include/c++/10/bits/locale_classes.h:40,
from /usr/include/c++/10/bits/ios_base.h:41,
from /usr/include/c++/10/streambuf:41,
from /usr/include/c++/10/bits/streambuf_iterator.h:35,
from /usr/include/c++/10/iterator:66,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/10/ext/new_allocator.h:150:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/ext/new_allocator.h:150:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const AtomTypeData&}; _Tp = AtomTypeData; _Alloc = std::allocator<AtomTypeData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AtomTypeData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/c++/10/bits/c++allocator.h:33,
from /usr/include/c++/10/bits/allocator.h:46,
from /usr/include/c++/10/string:41,
from /usr/include/c++/10/bits/locale_classes.h:40,
from /usr/include/c++/10/bits/ios_base.h:41,
from /usr/include/c++/10/streambuf:41,
from /usr/include/c++/10/bits/streambuf_iterator.h:35,
from /usr/include/c++/10/iterator:66,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/10/ext/new_allocator.h: In member function 'void PreprocessingAtomTypes::renumberTypes(gmx::ArrayRef<InteractionsOfType>, gmx_mtop_t*, int*, bool)':
/usr/include/c++/10/ext/new_allocator.h:150:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/ext/new_allocator.h:150:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hizzie.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void copyPreprocessResidues(const PreprocessResidue&, PreprocessResidue*, t_symtab*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MoleculePatch&}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void mergeAtomModifications(const MoleculePatchDatabase&, MoleculePatchDatabase*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp: In constructor 'InteractionOfType::InteractionOfType(gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, const string&)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp:111:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
111 | InteractionOfType::InteractionOfType(gmx::ArrayRef<const int> atoms,
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp: In function 'void insert_mols(int, int, int, real, real, t_atoms*, t_symtab*, std::vector<gmx::BasicVector<double> >*, const std::set<int>&, const t_atoms&, gmx::ArrayRef<gmx::BasicVector<double> >, int, real (*)[3], const string&, const real*, RotationType)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp:166:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
166 | static void insert_mols(int nmol_insrt,
| ^~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<double> makeExclusionDistances(const t_atoms*, AtomProperties*, real, real)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp: In member function 'virtual int gmx::{anonymous}::InsertMolecules::run()':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp:584:16: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
584 | insert_mols(nmolIns_, nmolTry_, seed_, defaultDistance_, scaleFactor_, &atoms, &top_.symtab,
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
585 | &x_, removableAtoms, atomsInserted, xInserted, ePBCForOutput, box_, positionFile_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
586 | deltaR_, enumRot_);
| ~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp: In function 'int nm2type(int, t_nm2type*, t_symtab*, t_atoms*, PreprocessingAtomTypes*, int*, InteractionsOfType*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp:342:87: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
342 | k = atype->addType(tab, atoms->atom[i], type, InteractionOfType({}, {}),
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp:342:87: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {MoleculePatch}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void read_h_db_file(const char*, std::vector<MoleculePatchDatabase>*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pgutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readir.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'void add_atom_to_restp(PreprocessResidue*, t_symtab*, int, const MoleculePatch*)':
/usr/include/c++/10/bits/vector.tcc:161:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
161 | _M_realloc_insert(begin() + (__position - cbegin()), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp: In function 'void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue>, gmx::ArrayRef<MoleculePatchDatabase>, t_atoms*, t_symtab*, gmx::ArrayRef<gmx::BasicVector<double> >, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:1305:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1305 | void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue> usedPpResidues,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function 'pull_t* set_pull_init(t_inputrec*, const gmx_mtop_t*, real (*)[3], real (*)[3], real, warninp_t)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:553:53: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
553 | bool groupObeysPbc = pullCheckPbcWithinGroup(
| ~~~~~~~~~~~~~~~~~~~~~~~^
554 | *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
555 | pbc, g, c_pullGroupSmallGroupThreshold);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:584:52: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
584 | groupObeysPbc = pullCheckPbcWithinGroup(
| ~~~~~~~~~~~~~~~~~~~~~~~^
585 | *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
586 | pbc, g, c_pullGroupPbcMargin);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readrot.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In function 'void sort_pdbatoms(gmx::ArrayRef<const PreprocessResidue>, int, t_atoms**, t_atoms**, std::vector<gmx::BasicVector<double> >*, t_blocka*, char***)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Distance = int; _Tp = InteractionOfType; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/stl_heap.h:424:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
424 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1666:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1666 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual int gmx::{anonymous}::pdb2gmx::run()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:2149:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2149 | match_atomnames_with_rtp(restp_chain, hb_chain, pdba, &symtab, x, bVerbose_);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp: In function 'void pdb2top(FILE*, const char*, const char*, t_atoms*, std::vector<gmx::BasicVector<double> >*, PreprocessingAtomTypes*, t_symtab*, gmx::ArrayRef<const PreprocessResidue>, gmx::ArrayRef<PreprocessResidue>, gmx::ArrayRef<MoleculePatchDatabase>, bool, bool, bool, const char*, real, gmx::ArrayRef<const DisulfideBond>, real, real, bool, bool, bool, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:782:26: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
782 | add_param(psb, ai, aj, {}, patch.s.c_str());
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:782:26: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:796:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
796 | add_param(psb, i, i + 1, {}, nullptr); /* C-O */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:796:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:797:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
797 | add_param(psb, i, i + 2, {}, nullptr); /* C-OA */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:797:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:798:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
798 | add_param(psb, i + 2, i + 3, {}, nullptr); /* OA-H */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:798:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:803:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
803 | add_param(psb, i, i + k + 1, {}, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:803:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:729:18: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
729 | add_param(ps, ai, aj, {}, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:729:18: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'int gmx_solvate(int, char**)':
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
1665 | _M_range_insert(__pos, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
1666 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
1665 | _M_range_insert(__pos, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
1666 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp: In function 'PreprocessingAtomTypes read_atype(const char*, t_symtab*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:93:67: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
93 | at.addType(tab, *a, name, InteractionOfType({}, {}), 0, 0);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:93:67: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'void readResidueDatabase(const string&, std::vector<PreprocessResidue>*, PreprocessingAtomTypes*, t_symtab*, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SpecialBond&}; _Tp = SpecialBond; _Alloc = std::allocator<SpecialBond>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<SpecialBond>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<SpecialBond> generateSpecialBonds()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SpecialBond*, std::vector<SpecialBond> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {MoleculePatch}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topdirs.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'void read_ter_db_file(const char*, std::vector<MoleculePatchDatabase>*, PreprocessingAtomTypes*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp: In function 'void convert_harmonics(gmx::ArrayRef<MoleculeInformation>, PreprocessingAtomTypes*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:231:68: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
231 | InteractionOfType(atoms, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:231:68: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp: In function 'void make_shake(gmx::ArrayRef<InteractionsOfType>, t_atoms*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:162:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | InteractionOfType(atomNumbers, forceParm));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:162:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:194:103: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
194 | add_param_to_list(&(plist[F_CONSTR]), InteractionOfType(atomNumbers, forceParm));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:194:103: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp: In function 'void print_bondeds(FILE*, int, Directive, int, int, gmx::ArrayRef<const InteractionsOfType>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:340:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
340 | atype.addType(&stab, *a, buf, InteractionOfType({}, {}), 0, 0);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:340:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp: In function 'char** read_topol(const char*, const char*, const char*, const char*, t_symtab*, PreprocessingAtomTypes*, std::vector<MoleculeInformation>*, std::unique_ptr<MoleculeInformation>*, gmx::ArrayRef<InteractionsOfType>, int*, double*, t_gromppopts*, real*, std::vector<gmx_molblock_t>*, bool*, bool, bool, bool, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:135:87: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
135 | pairs->interactionTypes.emplace_back(InteractionOfType(atomNumbers, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:135:87: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void add_param_to_list(InteractionsOfType*, const InteractionOfType&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void generate_LJCpairsNB(MoleculeInformation*, int, InteractionsOfType*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2658:106: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2658 | add_param_to_list(&mol->interactions[F_LJC_PAIRS_NB], InteractionOfType(atoms, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2658:106: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_at(t_symtab*, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, int, t_nbparam***, t_nbparam***, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:541:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
541 | InteractionOfType interactionType({}, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:541:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp: In function 'bool calc_vsite3_param(PreprocessingAtomTypes*, InteractionOfType*, t_atoms*, gmx::ArrayRef<const VsiteBondedInteraction>, gmx::ArrayRef<const VsiteBondedInteraction>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:402:13: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
402 | static bool calc_vsite3_param(PreprocessingAtomTypes* atypes,
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:402:13: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_vsitesn(Directive, gmx::ArrayRef<InteractionsOfType>, t_atoms*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2443:76: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2443 | add_param_to_list(&bond[ftype], InteractionOfType(atoms, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2443:76: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'int add_atomtype_decoupled(t_symtab*, PreprocessingAtomTypes*, t_nbparam***, t_nbparam***)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2574:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2574 | nr = at->addType(symtab, atom, "decoupled", InteractionOfType({}, forceParam, ""), -1, 0);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2574:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VsiteBondedInteraction}; _Tp = VsiteBondedInteraction; _Alloc = std::allocator<VsiteBondedInteraction>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VsiteBondedInteraction>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bond(Directive, gmx::ArrayRef<InteractionsOfType>, gmx::ArrayRef<InteractionsOfType>, t_atoms*, PreprocessingAtomTypes*, char*, bool, bool, real, bool, bool*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1984:50: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1984 | InteractionOfType param(atoms, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1984:50: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'void enter_bonded(int, std::vector<VsiteBondedInteraction>*, const InteractionOfType&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VsiteBondedInteraction*, std::vector<VsiteBondedInteraction> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp: In function 'int set_vsites(bool, t_atoms*, PreprocessingAtomTypes*, gmx::ArrayRef<InteractionsOfType>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:821:55: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
821 | bERROR = calc_vsite3_param(atypes, ¶m, atoms, allVsiteBondeds.bonds,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
822 | allVsiteBondeds.angles);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:821:55: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:821:55: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp: In function 'void lo_set_force_const(InteractionsOfType*, real*, int, bool, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:60: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | param = InteractionOfType(param.atoms(), forceParam);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:60: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_cmap(Directive, gmx::ArrayRef<InteractionsOfType>, gmx::ArrayRef<InteractionsOfType>, t_atoms*, PreprocessingAtomTypes*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2336:64: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2336 | InteractionOfType param(atoms, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2336:64: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void generate_nbparams(int, int, InteractionsOfType*, PreprocessingAtomTypes*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:103:105: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
103 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:103:105: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:127:105: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
127 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:127:105: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:151:105: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
151 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:151:105: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:184:97: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
184 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:184:97: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp: In function 'int gmx_x2top(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:137:76: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
137 | add_param_to_list(bond, InteractionOfType(atoms, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:137:76: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:60: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | param = InteractionOfType(param.atoms(), forceParam);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:60: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bondtype(InteractionsOfType*, const InteractionOfType&, int, int, bool, const char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:711:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
711 | InteractionOfType(b.atoms(), b.forceParam(), b.interactionTypeName()));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:711:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:730:103: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
730 | bt->interactionTypes.emplace_back(InteractionOfType(atoms, forceParam, b.interactionTypeName()));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:730:103: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bt(Directive, gmx::ArrayRef<InteractionsOfType>, int, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:851:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
851 | push_bondtype(&(bt[ftype]), InteractionOfType(atomTypes, forceParam), nral, ftype, FALSE, line, wi);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:851:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_dihedraltype(Directive, gmx::ArrayRef<InteractionsOfType>, PreprocessingBondAtomType*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1019:68: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1019 | push_bondtype(&(bt[ftype]), InteractionOfType(atoms, forceParam), 4, ftype, bAllowRepeat, line, wi);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1019:68: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'void push_cmaptype(Directive, gmx::ArrayRef<InteractionsOfType>, int, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, warninp*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1286:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1286 | push_bondtype(&(bt[ftype]), InteractionOfType(atomTypes, forceParam), nral, ftype, FALSE, line, wi);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1286:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/xlate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'void convert_pairs_to_pairsQ(gmx::ArrayRef<InteractionsOfType>, real, t_atoms*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2606:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2606 | paramnew.emplace_back(InteractionOfType(param.atoms(), forceParam, ""));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2606:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void clean_vsite_bondeds(gmx::ArrayRef<InteractionsOfType>, int, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:39:
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void low_do_four_core(int, real*, real*, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/crosscorr.cpp
/usr/include/c++/10/bits/stl_vector.h: In function 'void low_do_autocorr(const char*, const gmx_output_env_t*, const char*, int, int, int, real**, real, long unsigned int, int, gmx_bool, gmx_bool, gmx_bool, real, real, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/gmx_lmcurve.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/integrate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/polynomials.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/statistics/statistics.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/abstractdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/analysisdata.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function '_Z16many_auto_correlPSt6vectorIS_IdSaIdEESaIS1_EE._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'int many_auto_correl(std::vector<std::vector<double> >*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataproxy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::AbstractAnalysisArrayData::AbstractAnalysisArrayData()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/average.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/frameaverager.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/histogram.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/lifetime.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::AnalysisDataDisplacementModule::frameFinished(const gmx::AnalysisDataFrameHeader&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/plot.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::AnalysisDataValue&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::internal::AnalysisDataStorageFrameData::addPointSet(int, int, gmx::ArrayRef<const gmx::AnalysisDataValue>)':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:583:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
583 | void AnalysisDataStorageFrameData::addPointSet(int dataSetIndex,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:44:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::AnalysisDataStorageFrame::finishPointSet()':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:714:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
714 | data_->addPointSet(currentDataSet_, firstColumn,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
715 | makeConstArrayRef(values_).subArray(begin, end - begin));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:714:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/coordinatefile.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/outputselector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setforces.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setprecision.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setvelocities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::analysismodules::{anonymous}::Sasa::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/check.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/convert_tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/eneconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/make_ndx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/mk_angndx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/pme_error.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjcat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tune_pme.cpp
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp: In function 'int gmx_trjconv(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp:1245:66: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1245 | put_atoms_in_compact_unitcell(ePBC, ecenter, fr.box, positionsArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp:1245:66: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp:106:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
106 | void BoxDeformation::apply(ArrayRef<RVec> x, matrix box, int64_t step)
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(const t_commrec*, t_state*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef<gmx::BasicVector<double> >, const real*, const real*, int, double*, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp:50:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
50 | void calc_mu(int start,
| ^~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator<VerletbufAtomtype>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VerletbufAtomtype>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<VerletbufAtomtype> getVerletBufferAtomtypes(const gmx_mtop_t&, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
60 | static void constr_recur(const t_blocka* at2con,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 't_blocka gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:826:10: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
826 | t_blocka make_at2con(const gmx_moltype_t& moltype,
| ^~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:107:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
107 | DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp: In function 'void add_ebin_indexed(t_ebin*, int, gmx::ArrayRef<bool>, gmx::ArrayRef<const double>, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp:197:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
197 | void add_ebin_indexed(t_ebin* eb,
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::DispersionCorrection(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>, const interaction_const_t&, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:520:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
520 | DispersionCorrection::DispersionCorrection(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:530:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
530 | topParams_(mtop, inputrec, useBuckingham, numAtomTypes, nonbondedForceParameters)
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, real, const std::vector<bool>&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
810 | void andersen_tcoupl(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function 'void sum_dhdl(gmx_enerdata_t*, gmx::ArrayRef<const double>, const t_lambda&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:92:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
92 | void sum_dhdl(gmx_enerdata_t* enerd, gmx::ArrayRef<const real> lambda, const t_lambda& fepvals)
| ^~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp: In function 'void do_force_lowlevel(t_forcerec*, const t_inputrec*, const t_idef*, const t_commrec*, const gmx_multisim_t*, t_nrnb*, gmx_wallcycle_t, const t_mdatoms*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ForceOutputs*, gmx_enerdata_t*, t_fcdata*, const real (*)[3], const real*, const t_graph*, const real (*)[3], const gmx::StepWorkload&, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
290 | status = gmx_pme_do(
| ~~~~~~~~~~^
291 | fr->pmedata,
| ~~~~~~~~~~~~
292 | gmx::constArrayRefFromArray(coordinates.unpaddedConstArrayRef().data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | md->homenr - fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~
294 | forceWithVirial.force_, md->chargeA, md->chargeB, md->sqrt_c6A,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
295 | md->sqrt_c6B, md->sigmaA, md->sigmaB, box, cr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
296 | DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
297 | DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0, nrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
298 | ewaldOutput.vir_q, ewaldOutput.vir_lj, &Vlr_q, &Vlr_lj,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
299 | lambda[efptCOUL], lambda[efptVDW], &ewaldOutput.dvdl[efptCOUL],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
300 | &ewaldOutput.dvdl[efptVDW], pme_flags);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
325 | gmx_pme_calc_energy(
| ~~~~~~~~~~~~~~~~~~~^
326 | fr->pmedata,
| ~~~~~~~~~~~~
327 | coordinates.unpaddedConstArrayRef().subArray(md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
328 | gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
329 | &Vlr_q);
| ~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp: In member function 'void gmx::EnergyOutput::addDataAtEnergyStep(bool, bool, double, real, const gmx_enerdata_t*, const t_state*, const t_lambda*, const t_expanded*, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const gmx_ekindata_t*, const real*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp:881:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
881 | add_ebin_indexed(ebin_, ie_, gmx::ArrayRef<bool>(bEner_), enerd->term, bSum);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:39:
/usr/include/c++/10/bits/unique_ptr.h: In function 'void init_forcerec(FILE*, const gmx::MDLogger&, t_forcerec*, t_fcdata*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, real (*)[3], const char*, const char*, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, const gmx_hw_info_t&, const gmx_device_info_t*, bool, bool, real, gmx_wallcycle*)':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp: In function 'void setCurrentLambdasLocal(int64_t, const t_lambda*, const double*, gmx::ArrayRef<double>, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:400:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
400 | void setCurrentLambdasLocal(const int64_t step,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function 'void gmx::lincs_update_atoms(gmx::Lincs*, int, real, gmx::ArrayRef<const double>, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*, real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:445:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
445 | static void lincs_update_atoms(Lincs* li,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:445:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function '_ZN3gmx15constrain_lincsEbRK10t_inputrecxPNS_5LincsERK9t_mdatomsPK9t_commrecPK14gmx_multisim_tPA3_KdPA3_dSI_SG_P5t_pbcdPddSI_bSI_NS_18ConstraintVariableEP6t_nrnbiPi._omp_fn.1':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:708:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
708 | lincs_update_atoms(lincsd, th, 1.0, sol, r,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
709 | (econq != ConstraintVariable::Force) ? invmass : nullptr, fp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:708:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function '_ZN3gmx15constrain_lincsEbRK10t_inputrecxPNS_5LincsERK9t_mdatomsPK9t_commrecPK14gmx_multisim_tPA3_KdPA3_dSI_SG_P5t_pbcdPddSI_bSI_NS_18ConstraintVariableEP6t_nrnbiPi._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1079:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1079 | lincs_update_atoms(lincsd, th, 1.0, mlambda, r, invmass, xp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1141:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1141 | lincs_update_atoms(lincsd, th, 1.0, blc_sol, r, invmass, xp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1148:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1148 | lincs_update_atoms(lincsd, th, invdt, mlambda, r, invmass, v);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resize(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, int, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:257:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
257 | void mdoutf_write_to_trajectory_files(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:282:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
282 | dd_collect_vec(cr->dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:287:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
287 | dd_collect_vec(cr->dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:293:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
293 | dd_collect_vec(cr->dd, state_local, f_local,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
294 | gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(f_global), f_local.size()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::set_lincs(const t_idef&, const t_mdatoms&, bool, const t_commrec*, gmx::Lincs*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'int add_binr(t_bin*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
103 | int add_binr(t_bin* b, gmx::ArrayRef<const real> r)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'void extract_binr(t_bin*, int, gmx::ArrayRef<double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
160 | void extract_binr(t_bin* b, int index, gmx::ArrayRef<real> r)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, gmx::ImdSession*, pull_t*, int64_t, t_nrnb*, gmx_wallcycle_t, const gmx_localtop_t*, const real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, t_fcdata*, gmx::ArrayRef<double>, t_graph*, t_forcerec*, gmx::MdrunScheduleWorkload*, const gmx_vsite_t*, real*, double, gmx_edsam*, int, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:895:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
895 | void do_force(FILE* fplog,
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1070:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1070 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1103:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1103 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1154:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1154 | nbnxn_put_on_grid(nbv, box, 0, vzero, box_diag, nullptr, { 0, mdatoms->homenr }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1155 | fr->cginfo, x.unpaddedArrayRef(), 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1161:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1161 | nbnxn_put_on_grid_nonlocal(nbv, domdec_zones(cr->dd), fr->cginfo, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1243:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1243 | nbv->convertCoordinates(AtomLocality::Local, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1243:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1320:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1320 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1337:51: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1337 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1345:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1345 | nbv->convertCoordinates(AtomLocality::NonLocal, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1345:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1525:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1525 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
1526 | forceOut.forceWithShiftForces().shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1589:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1589 | stateGpu->copyForcesToGpu(forceOut.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1590 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1601:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1601 | stateGpu->copyForcesFromGpu(forceOut.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1602 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1613:57: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1613 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat, forceWithShiftForces.shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1634:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1634 | stateGpu->copyForcesToGpu(forceOut.forceWithShiftForces().force(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1771:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1771 | stateGpu->copyForcesToGpu(forceWithShift, locality);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1790:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1790 | stateGpu->copyForcesFromGpu(forceWithShift, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp: In member function 'void gmx::UpdateConstrainCuda::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
70 | void UpdateConstrainCuda::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp: In function 'void do_md_trajectory_writing(FILE*, t_commrec*, int, const t_filenm*, int64_t, int64_t, double, t_inputrec*, t_state*, t_state*, ObservablesHistory*, const gmx_mtop_t*, t_forcerec*, gmx_mdoutf_t, const gmx::EnergyOutput&, gmx_ekindata_t*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:56:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
56 | void do_md_trajectory_writing(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:143:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
143 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step, t,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
144 | state, state_global, observablesHistory, f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'void update_pcouple_after_coordinates(FILE*, int64_t, const t_inputrec*, const t_mdatoms*, const real (*)[3], const real (*)[3], const real (*)[3], real (*)[3], t_state*, t_nrnb*, gmx::Update*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1752:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1752 | upd->deform()->apply(localX, state->box, step);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp: In function 'gmx::RangePartitioning gmx::makeUpdateGroups(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp:338:26: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
338 | static RangePartitioning makeUpdateGroups(const gmx_moltype_t& moltype, gmx::ArrayRef<const t_iparams> iparams)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp: In member function 'void gmx::UpdateGroupsCog::addCogs(gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:80:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
80 | void UpdateGroupsCog::addCogs(gmx::ArrayRef<const int> globalAtomIndices,
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'gmx_bool update_randomize_velocities(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, const gmx::Update*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1868:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1868 | extern gmx_bool update_randomize_velocities(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1896:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1896 | andersen_tcoupl(ir, step, cr, md, v, rate, upd->sd()->randomize_group, upd->sd()->boltzfac);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1896:24: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::Update::Impl::Impl(const t_inputrec*, gmx::BoxDeformation*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::Update::setNumAtoms(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void constructVsitesGlobal(const gmx_mtop_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:741:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
741 | void constructVsitesGlobal(const gmx_mtop_t& mtop, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:741:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual const std::vector<double>& gmx::{anonymous}::UnitAmplitudes::operator()(const t_mdatoms&, gmx::ArrayRef<const int>)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoptions.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp: In constructor 'gmx::DensityFittingForceProvider::Impl::Impl(const gmx::DensityFittingParameters&, gmx::basic_mdspan<const float, gmx::extents<-1, -1, -1> >, const gmx::TranslateAndScale&, const gmx::LocalAtomSet&, int, double, const gmx::DensityFittingForceProviderState&)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:79:19: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
79 | scaleToLattice({ &sigmaInLatticeCoordinates, &sigmaInLatticeCoordinates + 1 });
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:166:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
166 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
167 | { &referenceDensityCenter_, &referenceDensityCenter_ + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:171:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
171 | transformationToDensityLattice_({ &referenceDensityOriginShift, &referenceDensityOriginShift + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:172:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
172 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | { &referenceDensityOriginShift, &referenceDensityOriginShift + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp: In member function 'void gmx::DensityFittingForceProvider::Impl::calculateForces(const gmx::ForceProviderInput&, gmx::ForceProviderOutput*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:210:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
210 | transformationToDensityLattice_(transformedCoordinates_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:258:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
258 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(forces_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingparameters.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function '_Z25split_vsites_over_threadsPK7t_ilistPK9t_iparamsPK9t_mdatomsP11gmx_vsite_t._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:551:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
551 | static void pme_load_balance(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_loadbal_do(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, t_forcerec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_wallcycle_t, int64_t, int64_t, gmx_bool*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:896:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
896 | void pme_loadbal_do(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:1035:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1035 | pme_load_balance(pme_lb, cr, fp_err, fp_log, mdlog, ir, box, x,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1036 | pme_lb->cycles_c - cycles_prev, fr->ic, fr->nbv.get(), &fr->pmedata, step);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'void gmx_pme_calc_energy(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const double>, real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:952:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
952 | void gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q, real* V)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:952:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:72:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:72:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'int gmx_pmeonly(gmx_pme_t*, const t_commrec*, t_nrnb*, gmx_wallcycle*, gmx_walltime_accounting_t, t_inputrec*, PmeRunMode)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:711:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
711 | stateGpu->copyCoordinatesToGpu(gmx::ArrayRef<gmx::RVec>(pme_pp->x), gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
728 | gmx_pme_do(pme, pme_pp->x, pme_pp->f, pme_pp->chargeA.data(), pme_pp->chargeB.data(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
729 | pme_pp->sqrt_c6A.data(), pme_pp->sqrt_c6B.data(), pme_pp->sigmaA.data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
730 | pme_pp->sigmaB.data(), box, cr, maxshift_x, maxshift_y, mynrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
731 | output.coulombVirial_, output.lennardJonesVirial_, &output.coulombEnergy_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
732 | &output.lennardJonesEnergy_, lambda_q, lambda_lj, &dvdlambda_q,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
733 | &dvdlambda_lj, pmeFlags);
| ~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void dd_pmeredist_f(gmx_pme_t*, PmeAtomComm*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:388:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
388 | void dd_pmeredist_f(struct gmx_pme_t* pme, PmeAtomComm* atc, gmx::ArrayRef<gmx::RVec> f, gmx_bool bAddF)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'int gmx_pme_do(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, real*, real*, real*, real*, real*, real*, const real (*)[3], const t_commrec*, int, int, t_nrnb*, gmx_wallcycle*, real (*)[3], real (*)[3], real*, real*, real, real, real*, real*, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1004:5: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1004 | int gmx_pme_do(struct gmx_pme_t* pme,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1004:5: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1154:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1154 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, coefficient);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1154:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1384:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1384 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, RedistC6);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1384:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1393:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1393 | do_redist_pos_coeffs(pme, cr, FALSE, coordinates, RedistSigma);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1393:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void do_redist_pos_coeffs(gmx_pme_t*, const t_commrec*, gmx_bool, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:453:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
453 | void do_redist_pos_coeffs(struct gmx_pme_t* pme,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:545:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
545 | dd_collect_vec(cr->dd, &state->s, state->s.x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp: In member function 'void gmx::LegacySimulator::do_mimic()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:227:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
227 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:379:35: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
379 | setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:421:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
421 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
422 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
423 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
424 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
425 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
426 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:437:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
437 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
438 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
439 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
440 | fr, runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
441 | ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:451:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
451 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
452 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
453 | energyOutput, ekind, f, isCheckpointingStep, doRerun,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
454 | isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:509:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
509 | dd_collect_vec(cr->dd, state, flocal, ftemp);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:519:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
519 | mimicCommunicator.sendForces(ftemp, state_global->natoms);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:533:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
533 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void {anonymous}::EnergyEvaluator::run(em_state_t*, real*, real (*)[3], real (*)[3], int64_t, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:845:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
845 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, count, nrnb, wcycle,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
846 | top, ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
847 | ems->f.arrayRefWithPadding(), force_vir, mdAtoms->mdatoms(), enerd, fcd, ems->s.lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
848 | graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
849 | GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES | GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
850 | | (bNS ? GMX_FORCE_NS : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
851 | DDBalanceRegionHandler(cr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:905:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
905 | sum_dhdl(enerd, ems->s.lambda, *inputrec->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
253 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:749:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
749 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:753:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
753 | pme_loadbal_do(pme_loadbal, cr, (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
754 | fplog, mdlog, *ir, fr, state->box, state->x, wcycle, step, step_rel,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
755 | &bPMETunePrinting, simulationWork.useGpuPmePpCommunication);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:767:35: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
767 | setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:810:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
810 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:815:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
815 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:918:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
918 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
919 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
920 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
921 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
922 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
923 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:945:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
945 | do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
946 | nrnb, wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
947 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
948 | fr, runScheduleWork, vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
949 | (bNS ? GMX_FORCE_NS : 0) | force_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1100:25: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1100 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1128:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1128 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1136:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1136 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1152:40: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1152 | stateGpu->copyForcesFromGpu(ArrayRef<RVec>(f), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1159:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1159 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1160 | observablesHistory, top_global, fr, outf, energyOutput, ekind, f,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1161 | checkpointHandler->isCheckpointingStep(), bRerunMD, bLastStep,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1162 | mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1194:55: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1194 | bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, &upd, constr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1266:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1266 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1267:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1267 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1273:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1273 | stateGpu->copyForcesToGpu(ArrayRef<RVec>(f), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1280:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1280 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1281 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1282 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1283 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1290:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1290 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1393:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1393 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1429:55: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1429 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1437:58: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1437 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1455:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1455 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'bool do_em_step(const t_commrec*, t_inputrec*, t_mdatoms*, em_state_t*, real, PaddedHostVector<gmx::BasicVector<double> >*, em_state_t*, gmx::Constraints*, int64_t)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void init_em(FILE*, const gmx::MDLogger&, const char*, const t_commrec*, t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, gmx_mtop_t*, em_state_t*, gmx_localtop_t*, t_nrnb*, t_forcerec*, t_graph**, gmx::MDAtoms*, gmx_global_stat**, gmx_vsite_t*, gmx::Constraints*, gmx_shellfc_t**)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:385:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
385 | initialize_lambdas(fplog, *ir, MASTER(cr), &(state_global->fep_state), state_global->lambda, nullptr);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_lbfgs()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1858:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1858 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1859 | static_cast<real>(step), &ems.s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1860 | observablesHistory, ems.f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:52:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp: In member function 'void gmx::LegacySimulator::do_rerun()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:302:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
302 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:52:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:551:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
551 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
552 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
553 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
554 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
555 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
556 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:567:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
567 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
568 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
569 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
570 | fr, runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
571 | ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:581:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
581 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
582 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
583 | energyOutput, ekind, f, isCheckpointingStep, doRerun,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
584 | isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:641:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
641 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_nm()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:2766:40: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
2766 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, nullptr, step, inputrec,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2767 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2768 | fcd, state_work.s.natoms, state_work.s.x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2769 | state_work.s.v.arrayRefWithPadding(), state_work.s.box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2770 | state_work.s.lambda, &state_work.s.hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2771 | state_work.f.arrayRefWithPadding(), vir, mdatoms, nrnb,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2772 | wcycle, graph, shellfc, fr, runScheduleWork, t, mu_tot,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2773 | vsite, DDBalanceRegionHandler(nullptr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function 'void relax_shell_flexcon(FILE*, const t_commrec*, const gmx_multisim_t*, gmx_bool, gmx_enfrot*, int64_t, const t_inputrec*, gmx::ImdSession*, pull_t*, gmx_bool, int, const gmx_localtop_t*, gmx::Constraints*, gmx_enerdata_t*, t_fcdata*, int, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, const real (*)[3], gmx::ArrayRef<double>, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, t_nrnb*, gmx_wallcycle_t, t_graph*, gmx_shellfc_t*, t_forcerec*, gmx::MdrunScheduleWorkload*, double, real*, const gmx_vsite_t*, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:936:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
936 | void relax_shell_flexcon(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1094:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1094 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, mdstep,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1095 | nrnb, wcycle, top, box, x, hist, forceWithPadding[Min], force_vir, md, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1096 | lambda, graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1097 | (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1188:17: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1188 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, 1, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1189 | wcycle, top, box, posWithPadding[Try], hist, forceWithPadding[Try], force_vir, md,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1190 | enerd, fcd, lambda, graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1191 | shellfc_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_cg()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_steep()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::LegacySimulator::do_tpi()':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:591:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
591 | nbnxn_put_on_grid(fr->nbv.get(), box, 0, vzero, boxDiagonal, nullptr, { 0, a_tp0 }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
592 | fr->cginfo, x, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:663:34: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
663 | nbnxn_put_on_grid(fr->nbv.get(), box, 1, x_init, x_init, nullptr, { a_tp0, a_tp1 },
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
664 | -1, fr->cginfo, x, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:722:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
722 | fr->nbv->convertCoordinates(AtomLocality::NonLocal, false, x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:722:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:745:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
745 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
746 | wcycle, &top, state_global->box, state_global->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
747 | &state_global->hist, f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
748 | state_global->lambda, nullptr, fr, runScheduleWork, nullptr, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
749 | GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY | (bStateChanged ? GMX_FORCE_STATECHANGED : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
750 | DDBalanceRegionHandler(nullptr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/10/bits/unique_ptr.h: In member function 'int gmx::Mdrunner::mdrunner()':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:1395:38: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1395 | constructVsitesGlobal(mtop, globalState->x);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyCoordinatesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:132:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
132 | void StatePropagatorDataGpu::copyCoordinatesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_x */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyCoordinatesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:147:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
147 | void StatePropagatorDataGpu::copyCoordinatesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_x */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyVelocitiesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:164:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
164 | void StatePropagatorDataGpu::copyVelocitiesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_v */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyVelocitiesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:180:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
180 | void StatePropagatorDataGpu::copyVelocitiesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_v */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyForcesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:204:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
204 | void StatePropagatorDataGpu::copyForcesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_f */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyForcesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
229 | void StatePropagatorDataGpu::copyForcesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_f */,
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintpotential.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const int&}; _Tp = gmx::Site; _Alloc = std::allocator<gmx::Site>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::Site>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr<gmx::IRestraintPotential>, const std::vector<int>&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::Site*, std::vector<gmx::Site> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:271:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
271 | void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::RVec> forces, int natoms)
| ^~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 'void writeXpmAxis(FILE*, const char*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:809:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
809 | static void writeXpmAxis(FILE* out, const char* axis, ArrayRef<const real> label)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:114:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
114 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx_tng_add_mtop(gmx_tng_trajectory_t, const gmx_mtop_t*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/vmdio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<t_matrix> read_xpm_matrix(const char*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::internal::{anonymous}::computeMassesAndCharges(const gmx_mtop_t*, const gmx_ana_pos_t&, std::vector<double>*, std::vector<double>*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::internal::SelectionData::initializeMassesAndCharges(const gmx_mtop_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.5.0.0 ../../lib/libgromacs_d.so.5 ../../lib/libgromacs_d.so
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color=
Scanning dependencies of target gmx
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/gmx.cpp.o -c /<<PKGBUILDDIR>>/src/programs/gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/legacymodules.cpp.o -c /<<PKGBUILDDIR>>/src/programs/legacymodules.cpp
Scanning dependencies of target gmxapi
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/context.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/context.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/gmxapi.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/gmxapi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/md.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/md.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdsignals.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdsignals.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.5.0.0 /usr/lib/arm-linux-gnueabihf/libX11.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target gmx
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/session.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/session.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/status.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/system.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/version.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/tpr.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi_d.so.0 -o ../../../lib/libgmxapi_d.so.0.1.0 CMakeFiles/gmxapi.dir/context.cpp.o CMakeFiles/gmxapi.dir/exceptions.cpp.o CMakeFiles/gmxapi.dir/gmxapi.cpp.o CMakeFiles/gmxapi.dir/md.cpp.o CMakeFiles/gmxapi.dir/mdmodule.cpp.o CMakeFiles/gmxapi.dir/mdsignals.cpp.o CMakeFiles/gmxapi.dir/session.cpp.o CMakeFiles/gmxapi.dir/status.cpp.o CMakeFiles/gmxapi.dir/system.cpp.o CMakeFiles/gmxapi.dir/version.cpp.o CMakeFiles/gmxapi.dir/workflow.cpp.o CMakeFiles/gmxapi.dir/tpr.cpp.o ../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libgmxapi_d.so.0.1.0 ../../../lib/libgmxapi_d.so.0 ../../../lib/libgmxapi_d.so
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googletest /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -Dgtest_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googletest/include -I/<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=c++14 -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-all.cc
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp /<<PKGBUILDDIR>>/build/basic/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color=
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[ 65%] Built target gmxapi
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so -o ../../../../../lib/libgtest.so CMakeFiles/gtest.dir/src/gtest-all.cc.o -lpthread
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock -I/<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++14 -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googlemock/src/gmock-all.cc
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so -o ../../../../lib/libgmock.so CMakeFiles/gmock.dir/src/gmock-all.cc.o -lpthread ../../../../lib/libgtest.so -lpthread
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/testutils /<<PKGBUILDDIR>>/build/basic/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color=
Scanning dependencies of target testutils
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cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/cmdlinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/conftest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/conftest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/filematchers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/interactivetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/loggertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpi_printer.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpi_printer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/refdata.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/refdata_xml.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata_xml.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/simulationdatabase.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/simulationdatabase.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stdiohelper.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mdmodulenotification.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/terminationhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectoryreader.cpp
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/ebin.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 69%] Built target testutils-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 69%] Built target mdrun_test_infrastructure
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_grp_tcstat&}; _Tp = t_grp_tcstat; _Alloc = std::allocator<t_grp_tcstat>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_grp_tcstat>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::LeapFrogTestData::LeapFrogTestData(int, real, const real*, const real*, int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/defaultinitializationallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestrunners.cpp
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target applied_forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/enumerationhelpers.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target mdlib-test
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
Scanning dependencies of target domdec-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o
/usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target onlinehelp-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 71%] Built target applied_forces-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/fixedcapacityvector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 71%] Built target domdec-test
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
Scanning dependencies of target ewald-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fft-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 71%] Built target fft-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/gputest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/testhardwarecontexts.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 72%] Built target ewald-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
Scanning dependencies of target hardware-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
Scanning dependencies of target math-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 73%] Built target hardware-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 74%] Built target utility-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 74%] Built target mdrunutility-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdspan-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/accessor_policy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 74%] Built target gpu_utils-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extents.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfit.cpp
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extensions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/layouts.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/mdspan.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 75%] Built target onlinehelp-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/gausstransform.cpp
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
Scanning dependencies of target options-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pbcutil-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 76%] Built target mdspan-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/multidimarray.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 76%] Built target pbcutil-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
Scanning dependencies of target random-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
Scanning dependencies of target restraintpotential-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef<gmx::BasicVector<ValueType> >, int) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:69:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
69 | void fillInputContents(ArrayRef<BasicVector<T>> inputRef, int scaleFactor)
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 76%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
94 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
105 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
Scanning dependencies of target table-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 78%] Built target math-test
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
Scanning dependencies of target taskassignment-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_InternalCounterSequence_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Default_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Using40Rounds_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Fast_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:117:54: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
117 | const std::vector<uint64_t> bitsZero{ { 0, 0, 0, 0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:127:87: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
127 | 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:136:86: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
136 | 0xa4093822299f31d0ULL, 0x082efa98ec4e6c89ULL } };
| ^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 78%] Built target taskassignment-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color=
Scanning dependencies of target topology-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 79%] Built target options-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/mtop.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 79%] Built target table-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/symtab.cpp
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pull-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target random-test
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
Scanning dependencies of target awh-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target pull-test
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp
Scanning dependencies of target simd-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target topology-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
Scanning dependencies of target compat-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-unused-member-function -o CMakeFiles/compat-test.dir/optional.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/optional.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const float&, double, const float&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/string_view.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/string_view.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target awh-test
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxana-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target gmxana-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx3-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx2-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/optional.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/string_view.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target compat-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
Scanning dependencies of target pdb2gmx1-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 83%] Built target simd-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxpreprocess-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target pdb2gmx3-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genconf.cpp
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color=
Scanning dependencies of target correlations-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target pdb2gmx2-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genion.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/correlationdataset.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target pdb2gmx1-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genrestr.cpp
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test-shared
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/mock_datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 85%] Built target correlations-test
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target coordinateio-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/builder.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target energyanalysis-test
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/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 85%] Built target energyanalysis-test
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
Scanning dependencies of target tool-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadapters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o
/usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 85%] Built target analysisdata-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fileio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 86%] Built target gmxpreprocess-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcserializer.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 87%] Built target tool-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
Scanning dependencies of target selection-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setbothtime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/fileioxdrserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target fileio-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-modules-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/densityfittingmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/testmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 89%] Built target coordinateio-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/domain_decomposition.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 90%] Built target mdrun-modules-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-coordination-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/periodicactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 90%] Built target selection-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-io-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/exactcontinuation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 90%] Built target mdrun-mpi-coordination-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/dispersion_correction.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-output-test
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/outputfiles.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/simulator.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 91%] Built target mdrun-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-non-integrator-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 92%] Built target mdrun-output-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-tpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-io-test.dir/termination.cpp.o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 92%] Built target mdrun-io-test
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/simulator.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 92%] Built target mdrun-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target mdrun-tpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/normalmodes.cpp
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
Scanning dependencies of target gmxapi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simple_mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-test.dir/status.cpp.o CMakeFiles/gmxapi-test.dir/system.cpp.o CMakeFiles/gmxapi-test.dir/version.cpp.o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-test.dir/runner.cpp.o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target gmxapi-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-mpi-test
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/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target gmxapi-mpi-test
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target mdrun-non-integrator-test
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
Scanning dependencies of target commandline-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-mpi-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target workflow-details-mpi-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-test.dir/workflow.cpp.o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target workflow-details-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target mdrunutility-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target mdrunutility-mpi-test
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target trajectoryanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/average.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target analysisdata-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 97%] Built target commandline-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target trajectoryanalysis-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
(cd build/basic; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic/lib ctest -V || dpkg-architecture -i hurd-i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: TestUtilsUnitTests
1: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsUnitTests.xml"
1: Test timeout computed to be: 30
1: [==========] Running 59 tests from 5 test cases.
1: [----------] Global test environment set-up.
1: [----------] 10 tests from InteractiveTestHelperTest
1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (1 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (1 ms)
1: [----------] 10 tests from InteractiveTestHelperTest (15 ms total)
1:
1: [----------] 34 tests from ReferenceDataTest
1: [ RUN ] ReferenceDataTest.HandlesSimpleData
1: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringBlockData
1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesVectorData
1: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceData
1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectData
1: [ OK ] ReferenceDataTest.HandlesIncorrectData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingData
1: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedData
1: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnys
1: [ OK ] ReferenceDataTest.HandlesAnys (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesReadingValues
1: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms)
1: [----------] 34 tests from ReferenceDataTest (25 ms total)
1:
1: [----------] 7 tests from FloatingPointDifferenceTest
1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total)
1:
1: [----------] 4 tests from FloatingPointToleranceTest
1: [ RUN ] FloatingPointToleranceTest.UlpTolerance
1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total)
1:
1: [----------] 4 tests from XvgTests
1: [ RUN ] XvgTests.CreateFile
1: [ OK ] XvgTests.CreateFile (2 ms)
1: [ RUN ] XvgTests.CheckMissing
1: [ OK ] XvgTests.CheckMissing (1 ms)
1: [ RUN ] XvgTests.CheckExtra
1: [ OK ] XvgTests.CheckExtra (1 ms)
1: [ RUN ] XvgTests.ReadIncorrect
1: [ OK ] XvgTests.ReadIncorrect (2 ms)
1: [----------] 4 tests from XvgTests (6 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 59 tests from 5 test cases ran. (47 ms total)
1: [ PASSED ] 59 tests.
1/54 Test #1: TestUtilsUnitTests .................. Passed 0.07 sec
test 2
Start 2: TestUtilsMpiUnitTests
2: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml"
2: Test timeout computed to be: 30
2: [==========] Running 1 test from 1 test case.
2: [----------] Global test environment set-up.
2: [----------] 1 test from MpiSelfTest
2: [ RUN ] MpiSelfTest.Runs
2: [ OK ] MpiSelfTest.Runs (1 ms)
2: [----------] 1 test from MpiSelfTest (1 ms total)
2:
2: [----------] Global test environment tear-down
2: [==========] 1 test from 1 test case ran. (1 ms total)
2: [ PASSED ] 1 test.
2/54 Test #2: TestUtilsMpiUnitTests ............... Passed 0.02 sec
test 3
Start 3: UtilityUnitTests
3: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityUnitTests.xml"
3: Test timeout computed to be: 30
3: [==========] Running 347 tests from 56 test cases.
3: [----------] Global test environment set-up.
3: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.Move
3: [ OK ] AllocatorTest/0.Move (0 ms)
3: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/0 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<float, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.Move
3: [ OK ] AllocatorTest/1.Move (0 ms)
3: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/1 (0 ms total)
3:
3: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.Move
3: [ OK ] AllocatorTest/2.Move (0 ms)
3: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/2 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.Move
3: [ OK ] AllocatorTest/3.Move (0 ms)
3: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/3 (0 ms total)
3:
3: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.Move
3: [ OK ] AllocatorTest/4.Move (0 ms)
3: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/4 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.Move
3: [ OK ] AllocatorTest/5.Move (0 ms)
3: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/5 (0 ms total)
3:
3: [----------] 1 test from AllocatorUntypedTest
3: [ RUN ] AllocatorUntypedTest.Comparison
3: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
3: [----------] 1 test from AllocatorUntypedTest (0 ms total)
3:
3: [----------] 1 test from EmptyArrayRefTest
3: [ RUN ] EmptyArrayRefTest.IsEmpty
3: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyArrayRefTest (0 ms total)
3:
3: [----------] 1 test from EmptyConstArrayRefTest
3: [ RUN ] EmptyConstArrayRefTest.IsEmpty
3: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
3: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/0 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
3: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/1 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
3: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (1 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/2 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
3: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/3 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
3: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/4 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
3: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/5 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
3: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/6 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
3: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/7 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
3: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/8 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
3: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/9 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
3: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/10 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
3: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/11 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
3: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/12 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
3: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/13 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
3: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/14 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
3: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/15 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
3: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/16 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
3: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/17 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
3: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/18 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
3: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/19 (0 ms total)
3:
3: [----------] 2 tests from CStringUtilityTest
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms)
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms)
3: [----------] 2 tests from CStringUtilityTest (0 ms total)
3:
3: [----------] 2 tests from DefaultInitializationAllocator
3: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms)
3: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms)
3: [----------] 2 tests from DefaultInitializationAllocator (0 ms total)
3:
3: [----------] 4 tests from EnumerationHelpersTest
3: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks
3: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe
3: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms)
3: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms)
3: [----------] 4 tests from EnumerationHelpersTest (1 ms total)
3:
3: [----------] 9 tests from FixedCapacityVectorTest
3: [ RUN ] FixedCapacityVectorTest.IsEmpty
3: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PushWorks
3: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PopWorks
3: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ClearWorks
3: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks
3: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.AtThrows
3: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms)
3: [ RUN ] FixedCapacityVectorTest.IteratorWorks
3: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks
3: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks
3: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms)
3: [----------] 9 tests from FixedCapacityVectorTest (0 ms total)
3:
3: [----------] 5 tests from InMemorySerializerTest
3: [ RUN ] InMemorySerializerTest.Roundtrip
3: [ OK ] InMemorySerializerTest.Roundtrip (0 ms)
3: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap
3: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SizeIsCorrect
3: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms)
3: [----------] 5 tests from InMemorySerializerTest (0 ms total)
3:
3: [----------] 4 tests from KeyValueTreeSerializerTest
3: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
3: [ OK ] KeyValueTreeSerializerTest.EmptyTree (1 ms)
3: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
3: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (1 ms)
3: [----------] 4 tests from KeyValueTreeSerializerTest (2 ms total)
3:
3: [----------] 6 tests from TreeValueTransformTest
3: [ RUN ] TreeValueTransformTest.SimpleTransforms
3: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
3: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
3: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (1 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromString
3: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
3: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms)
3: [ RUN ] TreeValueTransformTest.ScopedTransformRules
3: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms)
3: [----------] 6 tests from TreeValueTransformTest (1 ms total)
3:
3: [----------] 1 test from TreeValueTransformErrorTest
3: [ RUN ] TreeValueTransformErrorTest.ConversionError
3: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms)
3: [----------] 1 test from TreeValueTransformErrorTest (0 ms total)
3:
3: [----------] 7 tests from LoggerTest
3: [ RUN ] LoggerTest.EmptyLoggerWorks
3: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
3: [ RUN ] LoggerTest.LogsToStream
3: [ OK ] LoggerTest.LogsToStream (0 ms)
3: [ RUN ] LoggerTest.LogsToFile
3: [ OK ] LoggerTest.LogsToFile (1 ms)
3: [ RUN ] LoggerTest.LevelFilteringWorks
3: [ OK ] LoggerTest.LevelFilteringWorks (0 ms)
3: [ RUN ] LoggerTest.LogsToMultipleStreams
3: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms)
3: [ RUN ] LoggerTest.LogsToMultipleFiles
3: [ OK ] LoggerTest.LogsToMultipleFiles (2 ms)
3: [ RUN ] LoggerTest.LogsToStreamAndFile
3: [ OK ] LoggerTest.LogsToStreamAndFile (0 ms)
3: [----------] 7 tests from LoggerTest (3 ms total)
3:
3: [----------] 4 tests from MutexBasicTest
3: [ RUN ] MutexBasicTest.CanBeMade
3: [ OK ] MutexBasicTest.CanBeMade (0 ms)
3: [ RUN ] MutexBasicTest.CanBeLocked
3: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeTryLocked
3: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
3: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
3: [----------] 4 tests from MutexBasicTest (0 ms total)
3:
3: [----------] 3 tests from MutexTaskTest
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (0 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
3: [----------] 3 tests from MutexTaskTest (0 ms total)
3:
3: [----------] 2 tests from PathTest
3: [ RUN ] PathTest.StripSourcePrefixWorks
3: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
3: [ RUN ] PathTest.SearchOperationsWork
3: [ OK ] PathTest.SearchOperationsWork (1 ms)
3: [----------] 2 tests from PathTest (2 ms total)
3:
3: [----------] 2 tests from PhysicalNodeCommunicatorTest
3: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
3: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
3: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
3: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
3: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
3:
3: [----------] 9 tests from StringUtilityTest
3: [ RUN ] StringUtilityTest.StartsWith
3: [ OK ] StringUtilityTest.StartsWith (0 ms)
3: [ RUN ] StringUtilityTest.EndsWith
3: [ OK ] StringUtilityTest.EndsWith (0 ms)
3: [ RUN ] StringUtilityTest.StripSuffixIfPresent
3: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms)
3: [ RUN ] StringUtilityTest.StripString
3: [ OK ] StringUtilityTest.StripString (0 ms)
3: [ RUN ] StringUtilityTest.SplitString
3: [ OK ] StringUtilityTest.SplitString (0 ms)
3: [ RUN ] StringUtilityTest.SplitDelimitedString
3: [ OK ] StringUtilityTest.SplitDelimitedString (1 ms)
3: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
3: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms)
3: [----------] 9 tests from StringUtilityTest (2 ms total)
3:
3: [----------] 2 tests from FormatStringTest
3: [ RUN ] FormatStringTest.HandlesBasicFormatting
3: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
3: [ RUN ] FormatStringTest.HandlesLongStrings
3: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
3: [----------] 2 tests from FormatStringTest (0 ms total)
3:
3: [----------] 1 test from StringFormatterTest
3: [ RUN ] StringFormatterTest.HandlesBasicFormatting
3: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
3: [----------] 1 test from StringFormatterTest (0 ms total)
3:
3: [----------] 1 test from formatAndJoinTest
3: [ RUN ] formatAndJoinTest.Works
3: [ OK ] formatAndJoinTest.Works (0 ms)
3: [----------] 1 test from formatAndJoinTest (0 ms total)
3:
3: [----------] 1 test from JoinStringsTest
3: [ RUN ] JoinStringsTest.Works
3: [ OK ] JoinStringsTest.Works (0 ms)
3: [----------] 1 test from JoinStringsTest (0 ms total)
3:
3: [----------] 6 tests from ReplaceAllTest
3: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
3: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesNoMatches
3: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
3: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
3: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
3: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
3: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
3: [----------] 6 tests from ReplaceAllTest (0 ms total)
3:
3: [----------] 10 tests from TextLineWrapperTest
3: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
3: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
3: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
3: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectly
3: [ OK ] TextLineWrapperTest.WrapsCorrectly (1 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndent
3: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
3: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
3: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
3: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (1 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms)
3: [----------] 10 tests from TextLineWrapperTest (2 ms total)
3:
3: [----------] 6 tests from TextWriterTest
3: [ RUN ] TextWriterTest.WritesLines
3: [ OK ] TextWriterTest.WritesLines (0 ms)
3: [ RUN ] TextWriterTest.WritesLinesInParts
3: [ OK ] TextWriterTest.WritesLinesInParts (0 ms)
3: [ RUN ] TextWriterTest.WritesWrappedLines
3: [ OK ] TextWriterTest.WritesWrappedLines (0 ms)
3: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
3: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms)
3: [ RUN ] TextWriterTest.TracksNewlines
3: [ OK ] TextWriterTest.TracksNewlines (0 ms)
3: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
3: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms)
3: [----------] 6 tests from TextWriterTest (1 ms total)
3:
3: [----------] 1 test from TypeTraitsTest
3: [ RUN ] TypeTraitsTest.IsIntegralConstant
3: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
3: [----------] 1 test from TypeTraitsTest (0 ms total)
3:
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (1 ms total)
3:
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total)
3:
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (1 ms total)
3:
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (1 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (1 ms total)
3:
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms)
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (3 ms total)
3:
3: [----------] Global test environment tear-down
3: [==========] 347 tests from 56 test cases ran. (35 ms total)
3: [ PASSED ] 347 tests.
3/54 Test #3: UtilityUnitTests .................... Passed 0.09 sec
test 4
Start 4: UtilityMpiUnitTests
4: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml"
4: Test timeout computed to be: 30
4: [==========] Running 2 tests from 1 test case.
4: [----------] Global test environment set-up.
4: [----------] 2 tests from PhysicalNodeCommunicatorTest
4: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
4: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (1 ms)
4: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
4: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (1 ms)
4: [----------] 2 tests from PhysicalNodeCommunicatorTest (2 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 2 tests from 1 test case ran. (2 ms total)
4: [ PASSED ] 2 tests.
4/54 Test #4: UtilityMpiUnitTests ................. Passed 0.02 sec
test 5
Start 5: MdlibUnitTest
5: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdlibUnitTest.xml"
5: Test timeout computed to be: 30
5: [==========] Running 149 tests from 11 test cases.
5: [----------] Global test environment set-up.
5: [----------] 1 test from VerletBufferConstraintTest
5: [ RUN ] VerletBufferConstraintTest.EqualMasses
5: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms)
5: [----------] 1 test from VerletBufferConstraintTest (0 ms total)
5:
5: [----------] 2 tests from PrEbinTest
5: [ RUN ] PrEbinTest.HandlesAverages
5: [ OK ] PrEbinTest.HandlesAverages (1 ms)
5: [ RUN ] PrEbinTest.HandlesEmptyAverages
5: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms)
5: [----------] 2 tests from PrEbinTest (1 ms total)
5:
5: [----------] 4 tests from ShakeTest
5: [ RUN ] ShakeTest.ConstrainsOneBond
5: [ OK ] ShakeTest.ConstrainsOneBond (0 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
5: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (1 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
5: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms)
5: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
5: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
5: [----------] 4 tests from ShakeTest (1 ms total)
5:
5: [----------] 1 test from NullSignalTest
5: [ RUN ] NullSignalTest.NullSignallerWorks
5: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
5: [----------] 1 test from NullSignalTest (0 ms total)
5:
5: [----------] 7 tests from SignalTest
5: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
5: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
5: [----------] 7 tests from SignalTest (0 ms total)
5:
5: [----------] 9 tests from UpdateGroups
5: [ RUN ] UpdateGroups.ethaneUA
5: [ OK ] UpdateGroups.ethaneUA (0 ms)
5: [ RUN ] UpdateGroups.methane
5: [ OK ] UpdateGroups.methane (0 ms)
5: [ RUN ] UpdateGroups.ethane
5: [ OK ] UpdateGroups.ethane (0 ms)
5: [ RUN ] UpdateGroups.butaneUA
5: [ OK ] UpdateGroups.butaneUA (0 ms)
5: [ RUN ] UpdateGroups.waterThreeSite
5: [ OK ] UpdateGroups.waterThreeSite (0 ms)
5: [ RUN ] UpdateGroups.waterFourSite
5: [ OK ] UpdateGroups.waterFourSite (0 ms)
5: [ RUN ] UpdateGroups.fourAtomsWithSettle
5: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
5: [ RUN ] UpdateGroups.waterFlexAngle
5: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
5: [ RUN ] UpdateGroups.twoMoltypes
5: [ OK ] UpdateGroups.twoMoltypes (0 ms)
5: [----------] 9 tests from UpdateGroups (1 ms total)
5:
5: [----------] 1 test from UpdateGroupsCog
5: [ RUN ] UpdateGroupsCog.ComputesCogs
5: [ OK ] UpdateGroupsCog.ComputesCogs (1 ms)
5: [----------] 1 test from UpdateGroupsCog (1 ms total)
5:
5: [----------] 84 tests from WithParameters/ConstraintsTest
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/2
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/3
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/20
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/21
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/22
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/23
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 (0 ms)
5: [----------] 84 tests from WithParameters/ConstraintsTest (12 ms total)
5:
5: [----------] 11 tests from WithParameters/EnergyOutputTest
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (7 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (4 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (7 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3
5: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (2 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file
5:
Reading energy frame 0 time 10.100
Reading energy frame 1 time 27.500
Reading energy frame 2 time 44.900
Reading energy frame 3 time 62.300
Reading energy frame 4 time 79.700
Reading energy frame 5 time 97.100
Reading energy frame 6 time 114.500
Reading energy frame 7 time 131.900
Reading energy frame 8 time 149.300
Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (24 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (8 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (7 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (7 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (8 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (7 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (7 ms)
5: [----------] 11 tests from WithParameters/EnergyOutputTest (97 ms total)
5:
5: [----------] 16 tests from WithParameters/LeapFrogTest
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (8 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (3 ms)
5: [----------] 16 tests from WithParameters/LeapFrogTest (39 ms total)
5:
5: [----------] 13 tests from WithParameters/SettleTest
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (2 ms)
5: [----------] 13 tests from WithParameters/SettleTest (15 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 149 tests from 11 test cases ran. (168 ms total)
5: [ PASSED ] 149 tests.
5/54 Test #5: MdlibUnitTest ....................... Passed 0.20 sec
test 6
Start 6: AppliedForcesUnitTest
6: Test command: /<<PKGBUILDDIR>>/build/basic/bin/applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml"
6: Test timeout computed to be: 30
6: [==========] Running 20 tests from 4 test cases.
6: [----------] Global test environment set-up.
6: [----------] 2 tests from DensityFittingTest
6: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows
6: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (1 ms)
6: [ RUN ] DensityFittingTest.SingleAtom
6: [ OK ] DensityFittingTest.SingleAtom (1 ms)
6: [----------] 2 tests from DensityFittingTest (2 ms total)
6:
6: [----------] 8 tests from DensityFittingOptionsTest
6: [ RUN ] DensityFittingOptionsTest.DefaultParameters
6: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OptionSetsActive
6: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive
6: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive
6: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (1 ms)
6: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup
6: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (0 ms)
6: [ RUN ] DensityFittingOptionsTest.InternalsToKvt
6: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms)
6: [ RUN ] DensityFittingOptionsTest.KvtToInternal
6: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms)
6: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent
6: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (1 ms)
6: [----------] 8 tests from DensityFittingOptionsTest (2 ms total)
6:
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest
6: [ RUN ] DensityFittingAmplitudeLookupTest.Unity
6: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Charge
6: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Masses
6: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms)
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total)
6:
6: [----------] 3 tests from ElectricFieldTest
6: [ RUN ] ElectricFieldTest.Static
6: [ OK ] ElectricFieldTest.Static (0 ms)
6: [ RUN ] ElectricFieldTest.Oscillating
6: [ OK ] ElectricFieldTest.Oscillating (1 ms)
6: [ RUN ] ElectricFieldTest.Pulsed
6: [ OK ] ElectricFieldTest.Pulsed (0 ms)
6: [----------] 3 tests from ElectricFieldTest (1 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 20 tests from 4 test cases ran. (5 ms total)
6: [ PASSED ] 20 tests.
6/54 Test #6: AppliedForcesUnitTest ............... Passed 0.02 sec
test 7
Start 7: CommandLineUnitTests
7: Test command: /<<PKGBUILDDIR>>/build/basic/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CommandLineUnitTests.xml"
7: Test timeout computed to be: 30
7: [==========] Running 59 tests from 7 test cases.
7: [----------] Global test environment set-up.
7: [----------] 3 tests from CommandLineHelpModuleTest
7: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
7: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms)
7: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
7: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms)
7: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
7: [ OK ] CommandLineHelpModuleTest.ExportsHelp (3 ms)
7: [----------] 3 tests from CommandLineHelpModuleTest (5 ms total)
7:
7: [----------] 7 tests from CommandLineHelpWriterTest
7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
7: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (1 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
7: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
7: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (1 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
7: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
7: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
7: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues
7: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms)
7: [----------] 7 tests from CommandLineHelpWriterTest (3 ms total)
7:
7: [----------] 6 tests from CommandLineModuleManagerTest
7: [ RUN ] CommandLineModuleManagerTest.RunsModule
7: [ OK ] CommandLineModuleManagerTest.RunsModule (1 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (1 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (1 ms)
7: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
7: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms)
7: [----------] 6 tests from CommandLineModuleManagerTest (3 ms total)
7:
7: [----------] 13 tests from CommandLineParserTest
7: [ RUN ] CommandLineParserTest.HandlesSingleValues
7: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
7: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
7: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
7: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
7: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (1 ms)
7: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
7: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesString
7: [ OK ] CommandLineParserTest.HandlesString (0 ms)
7: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
7: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
7: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
7: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
7: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
7: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
7: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms)
7: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
7: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
7: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
7: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (1 ms)
7: [----------] 13 tests from CommandLineParserTest (2 ms total)
7:
7: [----------] 6 tests from CommandLineProgramContextTest
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms)
7: [----------] 6 tests from CommandLineProgramContextTest (0 ms total)
7:
7: [----------] 3 tests from OutputNamesTest
7: [ RUN ] OutputNamesTest.CanBeSuffixed
7: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms)
7: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend
7: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms)
7: [ RUN ] OutputNamesTest.CanHavePartNumberAdded
7: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms)
7: [----------] 3 tests from OutputNamesTest (0 ms total)
7:
7: [----------] 21 tests from ParseCommonArgsTest
7: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
7: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (1 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
7: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
7: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
7: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
7: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
7: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
7: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
7: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
7: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
7: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (1 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
7: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
7: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms)
7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
7: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms)
7: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
7: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms)
7: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
7: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms)
7: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
7: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms)
7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms)
7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (1 ms)
7: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
7: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (1 ms)
7: [----------] 21 tests from ParseCommonArgsTest (7 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 59 tests from 7 test cases ran. (20 ms total)
7: [ PASSED ] 59 tests.
7/54 Test #7: CommandLineUnitTests ................ Passed 0.04 sec
test 8
Start 8: DomDecTests
8: Test command: /<<PKGBUILDDIR>>/build/basic/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/DomDecTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 9 tests from 2 test cases.
8: [----------] Global test environment set-up.
8: [----------] 7 tests from HashedMap
8: [ RUN ] HashedMap.InsertsFinds
8: [ OK ] HashedMap.InsertsFinds (0 ms)
8: [ RUN ] HashedMap.NegativeKeysWork
8: [ OK ] HashedMap.NegativeKeysWork (0 ms)
8: [ RUN ] HashedMap.InsertsErases
8: [ OK ] HashedMap.InsertsErases (0 ms)
8: [ RUN ] HashedMap.InsertsOrAssigns
8: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
8: [ RUN ] HashedMap.Clears
8: [ OK ] HashedMap.Clears (0 ms)
8: [ RUN ] HashedMap.LinkedEntries
8: [ OK ] HashedMap.LinkedEntries (0 ms)
8: [ RUN ] HashedMap.ResizesTable
8: [ OK ] HashedMap.ResizesTable (0 ms)
8: [----------] 7 tests from HashedMap (1 ms total)
8:
8: [----------] 2 tests from LocalAtomSetManager
8: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
8: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms)
8: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
8: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
8: [----------] 2 tests from LocalAtomSetManager (0 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 9 tests from 2 test cases ran. (1 ms total)
8: [ PASSED ] 9 tests.
8/54 Test #8: DomDecTests ......................... Passed 0.02 sec
test 9
Start 9: EwaldUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/basic/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EwaldUnitTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 257 tests from 10 test cases.
9: [----------] Global test environment set-up.
9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (6 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms)
9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (7 ms total)
9:
9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (3 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (3 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (3 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (3 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (3 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (3 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (3 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (11 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (4 ms)
9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (113 ms total)
9:
9: [----------] 144 tests from SaneInput/PmeGatherTest
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (1 ms)
9: [----------] 144 tests from SaneInput/PmeGatherTest (141 ms total)
9:
9: [----------] 16 tests from SaneInput/PmeSolveTest
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (3 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (3 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (3 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (1 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (1 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (3 ms)
9: [----------] 16 tests from SaneInput/PmeSolveTest (47 ms total)
9:
9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (3 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (2 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (1 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (2 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (2 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (2 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (1 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (1 ms)
9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (16 ms total)
9:
9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (5 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (4 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (3 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (3 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (4 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (4 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (3 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (2 ms)
9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (29 ms total)
9:
9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (3 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (3 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (3 ms)
9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (44 ms total)
9:
9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (3 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (5 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (3 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (4 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (4 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (5 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (3 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (3 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (4 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (4 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (5 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (5 ms)
9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (52 ms total)
9:
9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (3 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (3 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (3 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (5 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (6 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (6 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (3 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (4 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (5 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (6 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (7 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (8 ms)
9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (67 ms total)
9:
9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (8 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (10 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (13 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (15 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (19 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (22 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (9 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (9 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (13 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (14 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (17 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (20 ms)
9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (206 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 257 tests from 10 test cases ran. (746 ms total)
9: [ PASSED ] 257 tests.
9/54 Test #9: EwaldUnitTests ...................... Passed 0.83 sec
test 10
Start 10: FFTUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FFTUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 14 tests from 4 test cases.
10: [----------] Global test environment set-up.
10: [----------] 2 tests from ManyFFTTest
10: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
10: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (9 ms)
10: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
10: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (13 ms)
10: [----------] 2 tests from ManyFFTTest (23 ms total)
10:
10: [----------] 1 test from FFTTest
10: [ RUN ] FFTTest.Real2DLength18_15Test
10: [ OK ] FFTTest.Real2DLength18_15Test (5 ms)
10: [----------] 1 test from FFTTest (6 ms total)
10:
10: [----------] 1 test from FFFTest3D
10: [ RUN ] FFFTest3D.Real5_6_9
10: [ OK ] FFFTest3D.Real5_6_9 (3 ms)
10: [----------] 1 test from FFFTest3D (3 ms total)
10:
10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (2 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (3 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (2 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (8 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (12 ms)
10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (32 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 14 tests from 4 test cases ran. (64 ms total)
10: [ PASSED ] 14 tests.
10/54 Test #10: FFTUnitTests ........................ Passed 0.08 sec
test 11
Start 11: GpuUtilsUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 62 tests from 20 test cases.
11: [----------] Global test environment set-up.
11: [----------] 2 tests from ClfftInitializer
11: [ RUN ] ClfftInitializer.SingleInitializationWorks
11: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms)
11: [ RUN ] ClfftInitializer.TwoInitializationsWork
11: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms)
11: [----------] 2 tests from ClfftInitializer (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
11: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/0 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float
11: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/1 (1 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<float>
11: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
11: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/3 (0 ms total)
11:
11: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
11: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
11: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
11: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
11: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
11: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total)
11:
11: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float
11: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
11: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
11: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
11: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
11: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total)
11:
11: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<float>
11: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
11: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
11: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
11: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
11: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
11: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
11: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (1 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.Swap
11: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.Comparison
11: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/0 (1 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float
11: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
11: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.Swap
11: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.Comparison
11: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<float>
11: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
11: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.Swap
11: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.Comparison
11: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
11: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
11: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.Swap
11: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.Comparison
11: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float
11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<float>
11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total)
11:
11: [----------] 1 test from HostAllocatorUntypedTest
11: [ RUN ] HostAllocatorUntypedTest.Comparison
11: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
11: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
11:
11: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/0.Move
11: [ OK ] AllocatorTest/0.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/0 (0 ms total)
11:
11: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/1.Move
11: [ OK ] AllocatorTest/1.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/1 (1 ms total)
11:
11: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/2.Move
11: [ OK ] AllocatorTest/2.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/2 (0 ms total)
11:
11: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (1 ms)
11: [ RUN ] AllocatorTest/3.Move
11: [ OK ] AllocatorTest/3.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/3 (1 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 62 tests from 20 test cases ran. (5 ms total)
11: [ PASSED ] 62 tests.
11/54 Test #11: GpuUtilsUnitTests ................... Passed 0.03 sec
test 12
Start 12: HardwareUnitTests
12: Test command: /<<PKGBUILDDIR>>/build/basic/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/HardwareUnitTests.xml"
12: Test timeout computed to be: 30
12: [==========] Running 4 tests from 1 test case.
12: [----------] Global test environment set-up.
12: [----------] 4 tests from HardwareTopologyTest
12: [ RUN ] HardwareTopologyTest.Execute
12: [ OK ] HardwareTopologyTest.Execute (18 ms)
12: [ RUN ] HardwareTopologyTest.HwlocExecute
12: [ OK ] HardwareTopologyTest.HwlocExecute (16 ms)
12: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
12: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (18 ms)
12: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
12: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (17 ms)
12: [----------] 4 tests from HardwareTopologyTest (69 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 4 tests from 1 test case ran. (69 ms total)
12: [ PASSED ] 4 tests.
12/54 Test #12: HardwareUnitTests ................... Passed 0.09 sec
test 13
Start 13: MathUnitTests
13: Test command: /<<PKGBUILDDIR>>/build/basic/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MathUnitTests.xml"
13: Test timeout computed to be: 30
13: [==========] Running 204 tests from 29 test cases.
13: [----------] Global test environment set-up.
13: [----------] 1 test from EmptyArrayRefWithPaddingTest
13: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
13: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
13: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total)
13:
13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
13: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
13: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total)
13:
13: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
13: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
13: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
13: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
13: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
13: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total)
13:
13: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
13: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
13: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
13: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
13: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
13: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total)
13:
13: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
13: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
13: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
13: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
13: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
13: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total)
13:
13: [----------] 8 tests from TranslateAndScaleTest
13: [ RUN ] TranslateAndScaleTest.identityTransformation
13: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms)
13: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling
13: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (1 ms)
13: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation
13: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms)
13: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial
13: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingIdentity
13: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingNonTrivial
13: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero
13: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero
13: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (1 ms)
13: [----------] 8 tests from TranslateAndScaleTest (2 ms total)
13:
13: [----------] 12 tests from DensitySimilarityTest
13: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect
13: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect
13: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch
13: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms)
13: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch
13: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms)
13: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect
13: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero
13: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms)
13: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect
13: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect
13: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (1 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne
13: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (59 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated
13: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (59 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated
13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (142 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect
13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms)
13: [----------] 12 tests from DensitySimilarityTest (262 ms total)
13:
13: [----------] 6 tests from StructureSimilarityTest
13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
13: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
13: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
13: [----------] 6 tests from StructureSimilarityTest (0 ms total)
13:
13: [----------] 8 tests from ExponentialMovingAverage
13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero
13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms)
13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative
13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms)
13: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue
13: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms)
13: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue
13: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms)
13: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly
13: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms)
13: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing
13: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms)
13: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect
13: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms)
13: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree
13: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms)
13: [----------] 8 tests from ExponentialMovingAverage (0 ms total)
13:
13: [----------] 21 tests from FunctionTest
13: [ RUN ] FunctionTest.StaticLog2
13: [ OK ] FunctionTest.StaticLog2 (1 ms)
13: [ RUN ] FunctionTest.Log2I32Bit
13: [ OK ] FunctionTest.Log2I32Bit (0 ms)
13: [ RUN ] FunctionTest.Log2I64Bit
13: [ OK ] FunctionTest.Log2I64Bit (0 ms)
13: [ RUN ] FunctionTest.GreatestCommonDivisor
13: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
13: [ RUN ] FunctionTest.InvsqrtFloat
13: [ OK ] FunctionTest.InvsqrtFloat (1 ms)
13: [ RUN ] FunctionTest.InvsqrtDouble
13: [ OK ] FunctionTest.InvsqrtDouble (0 ms)
13: [ RUN ] FunctionTest.InvsqrtInteger
13: [ OK ] FunctionTest.InvsqrtInteger (0 ms)
13: [ RUN ] FunctionTest.InvcbrtFloat
13: [ OK ] FunctionTest.InvcbrtFloat (0 ms)
13: [ RUN ] FunctionTest.InvcbrtDouble
13: [ OK ] FunctionTest.InvcbrtDouble (1 ms)
13: [ RUN ] FunctionTest.InvcbrtInteger
13: [ OK ] FunctionTest.InvcbrtInteger (0 ms)
13: [ RUN ] FunctionTest.SixthrootFloat
13: [ OK ] FunctionTest.SixthrootFloat (0 ms)
13: [ RUN ] FunctionTest.SixthrootDouble
13: [ OK ] FunctionTest.SixthrootDouble (0 ms)
13: [ RUN ] FunctionTest.SixthrootInteger
13: [ OK ] FunctionTest.SixthrootInteger (0 ms)
13: [ RUN ] FunctionTest.InvsixthrootFloat
13: [ OK ] FunctionTest.InvsixthrootFloat (0 ms)
13: [ RUN ] FunctionTest.InvsixthrootDouble
13: [ OK ] FunctionTest.InvsixthrootDouble (0 ms)
13: [ RUN ] FunctionTest.InvsixthrootInteger
13: [ OK ] FunctionTest.InvsixthrootInteger (1 ms)
13: [ RUN ] FunctionTest.Powers
13: [ OK ] FunctionTest.Powers (0 ms)
13: [ RUN ] FunctionTest.ErfInvFloat
13: [ OK ] FunctionTest.ErfInvFloat (0 ms)
13: [ RUN ] FunctionTest.ErfInvDouble
13: [ OK ] FunctionTest.ErfInvDouble (0 ms)
13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
13: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms)
13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
13: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms)
13: [----------] 21 tests from FunctionTest (6 ms total)
13:
13: [----------] 4 tests from GaussianOn1DLattice
13: [ RUN ] GaussianOn1DLattice.sumsCloseToOne
13: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms)
13: [ RUN ] GaussianOn1DLattice.isCorrect
13: [ OK ] GaussianOn1DLattice.isCorrect (0 ms)
13: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero
13: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms)
13: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange
13: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms)
13: [----------] 4 tests from GaussianOn1DLattice (0 ms total)
13:
13: [----------] 9 tests from GaussTransformTest
13: [ RUN ] GaussTransformTest.isZeroUponConstruction
13: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms)
13: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss
13: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms)
13: [ RUN ] GaussTransformTest.isZeroAfterSettingZero
13: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms)
13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX
13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms)
13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY
13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms)
13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ
13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms)
13: [ RUN ] GaussTransformTest.complementaryGaussAddToZero
13: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms)
13: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues
13: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms)
13: [ RUN ] GaussTransformTest.view
13: [ OK ] GaussTransformTest.view (1 ms)
13: [----------] 9 tests from GaussTransformTest (1 ms total)
13:
13: [----------] 3 tests from DensityFittingForce
13: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity
13: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms)
13: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections
13: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms)
13: [ RUN ] DensityFittingForce.pullsTowardsDerivative
13: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms)
13: [----------] 3 tests from DensityFittingForce (0 ms total)
13:
13: [----------] 2 tests from InvertMatrixTest
13: [ RUN ] InvertMatrixTest.IdentityIsImpotent
13: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
13: [ RUN ] InvertMatrixTest.ComputesInverse
13: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
13: [----------] 2 tests from InvertMatrixTest (0 ms total)
13:
13: [----------] 2 tests from InvertBoxMatrixTest
13: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
13: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
13: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
13: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
13: [----------] 2 tests from InvertBoxMatrixTest (0 ms total)
13:
13: [----------] 15 tests from MatrixTest
13: [ RUN ] MatrixTest.canSetFromArray
13: [ OK ] MatrixTest.canSetFromArray (0 ms)
13: [ RUN ] MatrixTest.canSetStaticallyFromList
13: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms)
13: [ RUN ] MatrixTest.canConstructAndFill
13: [ OK ] MatrixTest.canConstructAndFill (0 ms)
13: [ RUN ] MatrixTest.canSetValues
13: [ OK ] MatrixTest.canSetValues (0 ms)
13: [ RUN ] MatrixTest.canCopyAssign
13: [ OK ] MatrixTest.canCopyAssign (0 ms)
13: [ RUN ] MatrixTest.canSwap
13: [ OK ] MatrixTest.canSwap (0 ms)
13: [ RUN ] MatrixTest.staticMultiDimArrayExtent
13: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms)
13: [ RUN ] MatrixTest.determinantWorks
13: [ OK ] MatrixTest.determinantWorks (0 ms)
13: [ RUN ] MatrixTest.noninvertableDeterminantIsZero
13: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms)
13: [ RUN ] MatrixTest.determinantOfDiagonalMatrix
13: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms)
13: [ RUN ] MatrixTest.traceWorks
13: [ OK ] MatrixTest.traceWorks (0 ms)
13: [ RUN ] MatrixTest.transposeWorks
13: [ OK ] MatrixTest.transposeWorks (0 ms)
13: [ RUN ] MatrixTest.transposeOfSymmetricMatrix
13: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms)
13: [ RUN ] MatrixTest.canCreateFromLegacyMatrix
13: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms)
13: [ RUN ] MatrixTest.canFillLegacyMatrix
13: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms)
13: [----------] 15 tests from MatrixTest (1 ms total)
13:
13: [----------] 25 tests from MultiDimArrayTest
13: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic
13: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic
13: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSetValuesInStatic
13: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic
13: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveConstructStatic
13: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic
13: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveAssignStatic
13: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic
13: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyConstructStatic
13: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic
13: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyAssignStatic
13: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic
13: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (1 ms)
13: [ RUN ] MultiDimArrayTest.canSwapStatic
13: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSwapDynamic
13: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent
13: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms)
13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent
13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms)
13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent
13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms)
13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue
13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms)
13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray
13: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms)
13: [ RUN ] MultiDimArrayTest.conversionToView
13: [ OK ] MultiDimArrayTest.conversionToView (0 ms)
13: [ RUN ] MultiDimArrayTest.conversionToConstView
13: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms)
13: [ RUN ] MultiDimArrayTest.viewBegin
13: [ OK ] MultiDimArrayTest.viewBegin (0 ms)
13: [ RUN ] MultiDimArrayTest.viewEnd
13: [ OK ] MultiDimArrayTest.viewEnd (0 ms)
13: [ RUN ] MultiDimArrayTest.constViewConstBegin
13: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms)
13: [ RUN ] MultiDimArrayTest.constViewConstEnd
13: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms)
13: [----------] 25 tests from MultiDimArrayTest (1 ms total)
13:
13: [----------] 4 tests from MultiDimArrayToMdSpanTest
13: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms)
13: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms)
13: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms)
13: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms)
13: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
13: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/0.CanCopyAssign
13: [ OK ] PaddedVectorTest/0.CanCopyAssign (1 ms)
13: [ RUN ] PaddedVectorTest/0.CanMoveAssign
13: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/0.CanSwap
13: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/0 (1 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
13: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/1.CanCopyAssign
13: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/1.CanMoveAssign
13: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/1.CanSwap
13: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/1 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
13: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/2.CanCopyAssign
13: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/2.CanMoveAssign
13: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/2.CanSwap
13: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/2 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
13: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/3.CanCopyAssign
13: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/3.CanMoveAssign
13: [ OK ] PaddedVectorTest/3.CanMoveAssign (1 ms)
13: [ RUN ] PaddedVectorTest/3.CanSwap
13: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/3 (1 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
13: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/4.CanCopyAssign
13: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/4.CanMoveAssign
13: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/4.CanSwap
13: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/4 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/5.CanCopyAssign
13: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/5.CanMoveAssign
13: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/5.CanSwap
13: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/5 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/6.CanCopyAssign
13: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/6.CanMoveAssign
13: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/6.CanSwap
13: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/6 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/7.CanCopyAssign
13: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/7.CanMoveAssign
13: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/7.CanSwap
13: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/7 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/8.CanCopyAssign
13: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/8.CanMoveAssign
13: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/8.CanSwap
13: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/8 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/9.CanCopyAssign
13: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/9.CanMoveAssign
13: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/9.CanSwap
13: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/9 (0 ms total)
13:
13: [----------] 37 tests from RVecTest
13: [ RUN ] RVecTest.CanBeStoredInVector
13: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
13: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
13: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
13: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
13: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
13: [ RUN ] RVecTest.WorksAsMutable_rvec
13: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
13: [ RUN ] RVecTest.WorksAs_rvec_Array
13: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
13: [ RUN ] RVecTest.CanAddRVecToRvec
13: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
13: [ RUN ] RVecTest.CanAddAssignRVecToRvec
13: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
13: [ RUN ] RVecTest.CanSubtractRVecFromRvec
13: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
13: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
13: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
13: [ RUN ] RVecTest.CanDotProductRVecByRvec
13: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
13: [ RUN ] RVecTest.CanCrossProductRVecByRvec
13: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
13: [ RUN ] RVecTest.CanDivideRVecInplace
13: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
13: [ RUN ] RVecTest.CanScaleRVec
13: [ OK ] RVecTest.CanScaleRVec (0 ms)
13: [ RUN ] RVecTest.CanDivideRVec
13: [ OK ] RVecTest.CanDivideRVec (0 ms)
13: [ RUN ] RVecTest.CanDoUnitvFromRVec
13: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
13: [ RUN ] RVecTest.CanSqLengthOfRVec
13: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanLengthOfRVec
13: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanCastToRVec
13: [ OK ] RVecTest.CanCastToRVec (0 ms)
13: [ RUN ] RVecTest.CanCastToDVec
13: [ OK ] RVecTest.CanCastToDVec (0 ms)
13: [ RUN ] RVecTest.CanLeftScalarMultiply
13: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
13: [ RUN ] RVecTest.CanRightScalarMultiply
13: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
13: [ RUN ] RVecTest.CanGetUnitvFromRVec
13: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
13: [ RUN ] RVecTest.CanGetSqLengthOfRVec
13: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanGetLengthOfRVec
13: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanDoCrossProductOfRVec
13: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
13: [ RUN ] RVecTest.CanDoDotProductOfRVec
13: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
13: [ RUN ] RVecTest.CanScaleByVector
13: [ OK ] RVecTest.CanScaleByVector (0 ms)
13: [ RUN ] RVecTest.asIVec
13: [ OK ] RVecTest.asIVec (0 ms)
13: [ RUN ] RVecTest.elementWiseMin
13: [ OK ] RVecTest.elementWiseMin (0 ms)
13: [ RUN ] RVecTest.elementWiseMax
13: [ OK ] RVecTest.elementWiseMax (0 ms)
13: [ RUN ] RVecTest.WorksAs_dvec_Reference
13: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
13: [ RUN ] RVecTest.WorksAs_ivec_Reference
13: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
13: [ RUN ] RVecTest.WorksAs_rvec_Reference
13: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
13: [ RUN ] RVecTest.CopyConstructorWorks
13: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
13: [ RUN ] RVecTest.CopyAssignmentWorks
13: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
13: [ RUN ] RVecTest.MoveConstructorWorks
13: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
13: [ RUN ] RVecTest.MoveAssignmentWorks
13: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
13: [----------] 37 tests from RVecTest (1 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 204 tests from 29 test cases ran. (281 ms total)
13: [ PASSED ] 204 tests.
13/54 Test #13: MathUnitTests ....................... Passed 0.31 sec
test 14
Start 14: MdrunUtilityUnitTests
14: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml"
14: Test timeout computed to be: 30
14: [==========] Running 17 tests from 1 test case.
14: [----------] Global test environment set-up.
14: [----------] 17 tests from ThreadAffinityTest
14: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
14: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
14: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
14: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms)
14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
14: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms)
14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
14: NOTE: Affinity setting failed.
14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (2 ms)
14: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
14: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (1 ms)
14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
14: NOTE: Affinity setting for 1/2 threads failed.
14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (3 ms)
14: [----------] 17 tests from ThreadAffinityTest (14 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 17 tests from 1 test case ran. (15 ms total)
14: [ PASSED ] 17 tests.
14/54 Test #14: MdrunUtilityUnitTests ............... Passed 0.04 sec
test 15
Start 15: MdrunUtilityMpiUnitTests
15: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
15: Test timeout computed to be: 30
15: [==========] Running 13 tests from 2 test cases.
15: [----------] Global test environment set-up.
15: [----------] 6 tests from ThreadAffinityMultiRankTest
15: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
15: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (6 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
15: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (7 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
15: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (6 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
15: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (1 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (7 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (4 ms)
15: [----------] 6 tests from ThreadAffinityMultiRankTest (31 ms total)
15:
15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (5 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (4 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (6 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (5 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (5 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (7 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (5 ms)
15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (37 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 13 tests from 2 test cases ran. (68 ms total)
15: [ PASSED ] 13 tests.
15/54 Test #15: MdrunUtilityMpiUnitTests ............ Passed 0.09 sec
test 16
Start 16: MDSpanTests
16: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdspan-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MDSpanTests.xml"
16: Test timeout computed to be: 30
16: [==========] Running 32 tests from 7 test cases.
16: [----------] Global test environment set-up.
16: [----------] 4 tests from BasicAccessorPolicy
16: [ RUN ] BasicAccessorPolicy.Decay
16: [ OK ] BasicAccessorPolicy.Decay (0 ms)
16: [ RUN ] BasicAccessorPolicy.Access
16: [ OK ] BasicAccessorPolicy.Access (0 ms)
16: [ RUN ] BasicAccessorPolicy.Offset
16: [ OK ] BasicAccessorPolicy.Offset (0 ms)
16: [ RUN ] BasicAccessorPolicy.CopyAccessor
16: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms)
16: [----------] 4 tests from BasicAccessorPolicy (1 ms total)
16:
16: [----------] 4 tests from ExtentsTest
16: [ RUN ] ExtentsTest.Construction
16: [ OK ] ExtentsTest.Construction (0 ms)
16: [ RUN ] ExtentsTest.PurelyStatic
16: [ OK ] ExtentsTest.PurelyStatic (0 ms)
16: [ RUN ] ExtentsTest.RankNought
16: [ OK ] ExtentsTest.RankNought (0 ms)
16: [ RUN ] ExtentsTest.Assignment
16: [ OK ] ExtentsTest.Assignment (0 ms)
16: [----------] 4 tests from ExtentsTest (0 ms total)
16:
16: [----------] 8 tests from MdSpanExtension
16: [ RUN ] MdSpanExtension.SlicingAllStatic
16: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms)
16: [ RUN ] MdSpanExtension.SlicingDynamic
16: [ OK ] MdSpanExtension.SlicingDynamic (0 ms)
16: [ RUN ] MdSpanExtension.SlicingAllStatic3D
16: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms)
16: [ RUN ] MdSpanExtension.SlicingEqualsView3D
16: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms)
16: [ RUN ] MdSpanExtension.additionWorks
16: [ OK ] MdSpanExtension.additionWorks (0 ms)
16: [ RUN ] MdSpanExtension.subtractionWorks
16: [ OK ] MdSpanExtension.subtractionWorks (0 ms)
16: [ RUN ] MdSpanExtension.multiplicationWorks
16: [ OK ] MdSpanExtension.multiplicationWorks (0 ms)
16: [ RUN ] MdSpanExtension.divisionWorks
16: [ OK ] MdSpanExtension.divisionWorks (0 ms)
16: [----------] 8 tests from MdSpanExtension (0 ms total)
16:
16: [----------] 3 tests from LayoutTests
16: [ RUN ] LayoutTests.LayoutRightConstruction
16: [ OK ] LayoutTests.LayoutRightConstruction (0 ms)
16: [ RUN ] LayoutTests.LayoutRightProperties
16: [ OK ] LayoutTests.LayoutRightProperties (0 ms)
16: [ RUN ] LayoutTests.LayoutRightOperator
16: [ OK ] LayoutTests.LayoutRightOperator (0 ms)
16: [----------] 3 tests from LayoutTests (0 ms total)
16:
16: [----------] 1 test from MdSpanTest
16: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly
16: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms)
16: [----------] 1 test from MdSpanTest (0 ms total)
16:
16: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan<int, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<int> >
16: [ RUN ] MdSpanTest/0.Rank
16: [ OK ] MdSpanTest/0.Rank (0 ms)
16: [ RUN ] MdSpanTest/0.DynamicRank
16: [ OK ] MdSpanTest/0.DynamicRank (0 ms)
16: [ RUN ] MdSpanTest/0.Extents
16: [ OK ] MdSpanTest/0.Extents (0 ms)
16: [ RUN ] MdSpanTest/0.Strides
16: [ OK ] MdSpanTest/0.Strides (0 ms)
16: [ RUN ] MdSpanTest/0.Properties
16: [ OK ] MdSpanTest/0.Properties (0 ms)
16: [ RUN ] MdSpanTest/0.Operator
16: [ OK ] MdSpanTest/0.Operator (0 ms)
16: [----------] 6 tests from MdSpanTest/0 (0 ms total)
16:
16: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan<float, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<float> >
16: [ RUN ] MdSpanTest/1.Rank
16: [ OK ] MdSpanTest/1.Rank (0 ms)
16: [ RUN ] MdSpanTest/1.DynamicRank
16: [ OK ] MdSpanTest/1.DynamicRank (0 ms)
16: [ RUN ] MdSpanTest/1.Extents
16: [ OK ] MdSpanTest/1.Extents (0 ms)
16: [ RUN ] MdSpanTest/1.Strides
16: [ OK ] MdSpanTest/1.Strides (0 ms)
16: [ RUN ] MdSpanTest/1.Properties
16: [ OK ] MdSpanTest/1.Properties (0 ms)
16: [ RUN ] MdSpanTest/1.Operator
16: [ OK ] MdSpanTest/1.Operator (0 ms)
16: [----------] 6 tests from MdSpanTest/1 (0 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 32 tests from 7 test cases ran. (2 ms total)
16: [ PASSED ] 32 tests.
16/54 Test #16: MDSpanTests ......................... Passed 0.02 sec
test 17
Start 17: OnlineHelpUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/basic/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 22 tests from 4 test cases.
17: [----------] Global test environment set-up.
17: [----------] 6 tests from TextTableFormatterTest
17: [ RUN ] TextTableFormatterTest.HandlesBasicCase
17: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms)
17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
17: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms)
17: [ RUN ] TextTableFormatterTest.HandlesIndentation
17: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms)
17: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
17: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms)
17: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
17: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms)
17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
17: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms)
17: [----------] 6 tests from TextTableFormatterTest (1 ms total)
17:
17: [----------] 3 tests from HelpManagerTest
17: [ RUN ] HelpManagerTest.HandlesRootTopic
17: [ OK ] HelpManagerTest.HandlesRootTopic (1 ms)
17: [ RUN ] HelpManagerTest.HandlesSubTopics
17: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms)
17: [ RUN ] HelpManagerTest.HandlesInvalidTopics
17: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms)
17: [----------] 3 tests from HelpManagerTest (1 ms total)
17:
17: [----------] 2 tests from HelpTopicFormattingTest
17: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
17: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms)
17: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
17: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms)
17: [----------] 2 tests from HelpTopicFormattingTest (0 ms total)
17:
17: [----------] 11 tests from HelpWriterContextTest
17: [ RUN ] HelpWriterContextTest.FormatsParagraphs
17: [ OK ] HelpWriterContextTest.FormatsParagraphs (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
17: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms)
17: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
17: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsLiteralText
17: [ OK ] HelpWriterContextTest.FormatsLiteralText (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
17: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
17: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsBulletList
17: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
17: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
17: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsGridTable
17: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsTitles
17: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms)
17: [----------] 11 tests from HelpWriterContextTest (4 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 22 tests from 4 test cases ran. (8 ms total)
17: [ PASSED ] 22 tests.
17/54 Test #17: OnlineHelpUnitTests ................. Passed 0.03 sec
test 18
Start 18: OptionsUnitTests
18: Test command: /<<PKGBUILDDIR>>/build/basic/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OptionsUnitTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 110 tests from 18 test cases.
18: [----------] Global test environment set-up.
18: [----------] 5 tests from AbstractOptionStorageTest
18: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
18: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms)
18: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
18: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms)
18: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
18: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms)
18: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
18: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms)
18: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
18: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (1 ms)
18: [----------] 5 tests from AbstractOptionStorageTest (3 ms total)
18:
18: [----------] 8 tests from FileNameOptionTest
18: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
18: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
18: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
18: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
18: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
18: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
18: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
18: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
18: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms)
18: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
18: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
18: [----------] 8 tests from FileNameOptionTest (0 ms total)
18:
18: [----------] 15 tests from FileNameOptionManagerTest
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
18: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (1 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
18: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
18: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
18: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
18: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms)
18: [----------] 15 tests from FileNameOptionManagerTest (2 ms total)
18:
18: [----------] 1 test from OptionsTest
18: [ RUN ] OptionsTest.FailsOnNonsafeStorage
18: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms)
18: [----------] 1 test from OptionsTest (0 ms total)
18:
18: [----------] 9 tests from OptionsAssignerTest
18: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
18: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
18: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
18: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
18: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesMissingValue
18: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesExtraValue
18: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesGroups
18: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesSections
18: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
18: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
18: [----------] 9 tests from OptionsAssignerTest (1 ms total)
18:
18: [----------] 4 tests from OptionsAssignerBooleanTest
18: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
18: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms)
18: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
18: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
18: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
18: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
18: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
18: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms)
18: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total)
18:
18: [----------] 13 tests from OptionsAssignerIntegerTest
18: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
18: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (1 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
18: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
18: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
18: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
18: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
18: [----------] 13 tests from OptionsAssignerIntegerTest (1 ms total)
18:
18: [----------] 5 tests from OptionsAssignerDoubleTest
18: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
18: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
18: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
18: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (1 ms)
18: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
18: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
18: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
18: [----------] 5 tests from OptionsAssignerDoubleTest (1 ms total)
18:
18: [----------] 9 tests from OptionsAssignerStringTest
18: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
18: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
18: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
18: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
18: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
18: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
18: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
18: [----------] 9 tests from OptionsAssignerStringTest (0 ms total)
18:
18: [----------] 6 tests from OptionsAssignerEnumTest
18: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
18: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
18: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
18: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
18: [----------] 6 tests from OptionsAssignerEnumTest (1 ms total)
18:
18: [----------] 8 tests from RepeatingOptionSectionTest
18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
18: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
18: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
18: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
18: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms)
18: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total)
18:
18: [----------] 1 test from TimeUnitManagerTest
18: [ RUN ] TimeUnitManagerTest.BasicOperations
18: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
18: [----------] 1 test from TimeUnitManagerTest (0 ms total)
18:
18: [----------] 4 tests from TimeUnitBehaviorTest
18: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
18: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
18: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
18: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
18: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
18: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
18: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
18: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms)
18: [----------] 4 tests from TimeUnitBehaviorTest (1 ms total)
18:
18: [----------] 2 tests from TreeValueSupportAssignTest
18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
18: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms)
18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
18: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
18: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total)
18:
18: [----------] 1 test from TreeValueSupportAssignErrorTest
18: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
18: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms)
18: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total)
18:
18: [----------] 5 tests from TreeValueSupportCheckTest
18: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
18: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
18: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
18: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
18: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total)
18:
18: [----------] 6 tests from TreeValueSupportAdjustTest
18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
18: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (1 ms)
18: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
18: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
18: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms)
18: [----------] 6 tests from TreeValueSupportAdjustTest (1 ms total)
18:
18: [----------] 8 tests from TreeValueSupportTest
18: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
18: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
18: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsInt64Option
18: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsStringOption
18: [ OK ] TreeValueSupportTest.SupportsStringOption (1 ms)
18: [ RUN ] TreeValueSupportTest.SupportsFloatOption
18: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
18: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption
18: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (1 ms)
18: [ RUN ] TreeValueSupportTest.SupportsEnumOption
18: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms)
18: [----------] 8 tests from TreeValueSupportTest (3 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 110 tests from 18 test cases ran. (15 ms total)
18: [ PASSED ] 110 tests.
18/54 Test #18: OptionsUnitTests .................... Passed 0.04 sec
test 19
Start 19: PbcutilUnitTest
19: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pbcutil-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/PbcutilUnitTest.xml"
19: Test timeout computed to be: 30
19: [==========] Running 3 tests from 2 test cases.
19: [----------] Global test environment set-up.
19: [----------] 1 test from PbcTest
19: [ RUN ] PbcTest.CalcShiftsWorks
19: [ OK ] PbcTest.CalcShiftsWorks (1 ms)
19: [----------] 1 test from PbcTest (1 ms total)
19:
19: [----------] 2 tests from PbcEnumsTest
19: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect
19: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms)
19: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect
19: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms)
19: [----------] 2 tests from PbcEnumsTest (0 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 3 tests from 2 test cases ran. (1 ms total)
19: [ PASSED ] 3 tests.
19/54 Test #19: PbcutilUnitTest ..................... Passed 0.02 sec
test 20
Start 20: RandomUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/basic/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RandomUnitTests.xml"
20: Test timeout computed to be: 30
20: [==========] Running 44 tests from 10 test cases.
20: [----------] Global test environment set-up.
20: [----------] 4 tests from ExponentialDistributionTest
20: [ RUN ] ExponentialDistributionTest.Output
20: [ OK ] ExponentialDistributionTest.Output (1 ms)
20: [ RUN ] ExponentialDistributionTest.Logical
20: [ OK ] ExponentialDistributionTest.Logical (0 ms)
20: [ RUN ] ExponentialDistributionTest.Reset
20: [ OK ] ExponentialDistributionTest.Reset (0 ms)
20: [ RUN ] ExponentialDistributionTest.AltParam
20: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from ExponentialDistributionTest (1 ms total)
20:
20: [----------] 4 tests from GammaDistributionTest
20: [ RUN ] GammaDistributionTest.Output
20: [ OK ] GammaDistributionTest.Output (0 ms)
20: [ RUN ] GammaDistributionTest.Logical
20: [ OK ] GammaDistributionTest.Logical (0 ms)
20: [ RUN ] GammaDistributionTest.Reset
20: [ OK ] GammaDistributionTest.Reset (0 ms)
20: [ RUN ] GammaDistributionTest.AltParam
20: [ OK ] GammaDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from GammaDistributionTest (0 ms total)
20:
20: [----------] 4 tests from NormalDistributionTest
20: [ RUN ] NormalDistributionTest.Output
20: [ OK ] NormalDistributionTest.Output (1 ms)
20: [ RUN ] NormalDistributionTest.Logical
20: [ OK ] NormalDistributionTest.Logical (0 ms)
20: [ RUN ] NormalDistributionTest.Reset
20: [ OK ] NormalDistributionTest.Reset (0 ms)
20: [ RUN ] NormalDistributionTest.AltParam
20: [ OK ] NormalDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from NormalDistributionTest (1 ms total)
20:
20: [----------] 1 test from SeedTest
20: [ RUN ] SeedTest.makeRandomSeed
20: [ OK ] SeedTest.makeRandomSeed (0 ms)
20: [----------] 1 test from SeedTest (0 ms total)
20:
20: [----------] 6 tests from TabulatedNormalDistributionTest
20: [ RUN ] TabulatedNormalDistributionTest.Output14
20: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.Output16
20: [ OK ] TabulatedNormalDistributionTest.Output16 (1 ms)
20: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
20: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.Logical
20: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.Reset
20: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.AltParam
20: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
20: [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total)
20:
20: [----------] 1 test from TabulatedNormalDistributionTableTest
20: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
20: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (3 ms)
20: [----------] 1 test from TabulatedNormalDistributionTableTest (3 ms total)
20:
20: [----------] 6 tests from ThreeFry2x64Test
20: [ RUN ] ThreeFry2x64Test.Logical
20: [ OK ] ThreeFry2x64Test.Logical (0 ms)
20: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
20: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms)
20: [ RUN ] ThreeFry2x64Test.Reseed
20: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
20: [ RUN ] ThreeFry2x64Test.Discard
20: [ OK ] ThreeFry2x64Test.Discard (0 ms)
20: [ RUN ] ThreeFry2x64Test.InvalidCounter
20: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms)
20: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
20: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
20: [----------] 6 tests from ThreeFry2x64Test (1 ms total)
20:
20: [----------] 4 tests from UniformIntDistributionTest
20: [ RUN ] UniformIntDistributionTest.Output
20: [ OK ] UniformIntDistributionTest.Output (0 ms)
20: [ RUN ] UniformIntDistributionTest.Logical
20: [ OK ] UniformIntDistributionTest.Logical (0 ms)
20: [ RUN ] UniformIntDistributionTest.Reset
20: [ OK ] UniformIntDistributionTest.Reset (0 ms)
20: [ RUN ] UniformIntDistributionTest.AltParam
20: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from UniformIntDistributionTest (0 ms total)
20:
20: [----------] 5 tests from UniformRealDistributionTest
20: [ RUN ] UniformRealDistributionTest.GenerateCanonical
20: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms)
20: [ RUN ] UniformRealDistributionTest.Output
20: [ OK ] UniformRealDistributionTest.Output (1 ms)
20: [ RUN ] UniformRealDistributionTest.Logical
20: [ OK ] UniformRealDistributionTest.Logical (0 ms)
20: [ RUN ] UniformRealDistributionTest.Reset
20: [ OK ] UniformRealDistributionTest.Reset (0 ms)
20: [ RUN ] UniformRealDistributionTest.AltParam
20: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
20: [----------] 5 tests from UniformRealDistributionTest (1 ms total)
20:
20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms)
20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (2 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 44 tests from 10 test cases ran. (10 ms total)
20: [ PASSED ] 44 tests.
20/54 Test #20: RandomUnitTests ..................... Passed 0.04 sec
test 21
Start 21: RestraintTests
21: Test command: /<<PKGBUILDDIR>>/build/basic/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RestraintTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 1 test from 1 test case.
21: [----------] Global test environment set-up.
21: [----------] 1 test from RestraintManager
21: [ RUN ] RestraintManager.restraintList
21: [ OK ] RestraintManager.restraintList (0 ms)
21: [----------] 1 test from RestraintManager (0 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 1 test from 1 test case ran. (0 ms total)
21: [ PASSED ] 1 test.
21/54 Test #21: RestraintTests ...................... Passed 0.02 sec
test 22
Start 22: TableUnitTests
22: Test command: /<<PKGBUILDDIR>>/build/basic/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TableUnitTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 16 tests from 2 test cases.
22: [----------] Global test environment set-up.
22: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
22: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
22: [ OK ] SplineTableTest/0.HandlesIncorrectInput (2 ms)
22: [ RUN ] SplineTableTest/0.Sinc
22: [ OK ] SplineTableTest/0.Sinc (2 ms)
22: [ RUN ] SplineTableTest/0.LJ12
22: [ OK ] SplineTableTest/0.LJ12 (26 ms)
22: [ RUN ] SplineTableTest/0.PmeCorrection
22: [ OK ] SplineTableTest/0.PmeCorrection (2 ms)
22: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
22: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms)
22: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
22: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (2 ms)
22: [ RUN ] SplineTableTest/0.TwoFunctions
22: [ OK ] SplineTableTest/0.TwoFunctions (51 ms)
22: [ RUN ] SplineTableTest/0.ThreeFunctions
22: [ OK ] SplineTableTest/0.ThreeFunctions (59 ms)
22: [----------] 8 tests from SplineTableTest/0 (145 ms total)
22:
22: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
22: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
22: [ OK ] SplineTableTest/1.HandlesIncorrectInput (2 ms)
22: [ RUN ] SplineTableTest/1.Sinc
22: [ OK ] SplineTableTest/1.Sinc (2 ms)
22: [ RUN ] SplineTableTest/1.LJ12
22: [ OK ] SplineTableTest/1.LJ12 (4 ms)
22: [ RUN ] SplineTableTest/1.PmeCorrection
22: [ OK ] SplineTableTest/1.PmeCorrection (2 ms)
22: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
22: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms)
22: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
22: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (2 ms)
22: [ RUN ] SplineTableTest/1.TwoFunctions
22: [ OK ] SplineTableTest/1.TwoFunctions (8 ms)
22: [ RUN ] SplineTableTest/1.ThreeFunctions
22: [ OK ] SplineTableTest/1.ThreeFunctions (9 ms)
22: [----------] 8 tests from SplineTableTest/1 (30 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 16 tests from 2 test cases ran. (175 ms total)
22: [ PASSED ] 16 tests.
22/54 Test #22: TableUnitTests ...................... Passed 0.19 sec
test 23
Start 23: TaskAssignmentUnitTests
23: Test command: /<<PKGBUILDDIR>>/build/basic/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 3 tests from 2 test cases.
23: [----------] Global test environment set-up.
23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest
23: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork
23: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (1 ms)
23: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid
23: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms)
23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (1 ms total)
23:
23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest
23: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow
23: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (1 ms)
23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (1 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 3 tests from 2 test cases ran. (2 ms total)
23: [ PASSED ] 3 tests.
23/54 Test #23: TaskAssignmentUnitTests ............. Passed 0.02 sec
test 24
Start 24: TopologyTest
24: Test command: /<<PKGBUILDDIR>>/build/basic/bin/topology-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TopologyTest.xml"
24: Test timeout computed to be: 30
24: [==========] Running 11 tests from 3 test cases.
24: [----------] Global test environment set-up.
24: [----------] 3 tests from ExclusionBlockTest
24: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks
24: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms)
24: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka
24: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms)
24: [ RUN ] ExclusionBlockTest.MergeExclusions
24: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms)
24: [----------] 3 tests from ExclusionBlockTest (0 ms total)
24:
24: [----------] 2 tests from MtopTest
24: [ RUN ] MtopTest.RangeBasedLoop
24: [ OK ] MtopTest.RangeBasedLoop (0 ms)
24: [ RUN ] MtopTest.Operators
24: [ OK ] MtopTest.Operators (0 ms)
24: [----------] 2 tests from MtopTest (0 ms total)
24:
24: [----------] 6 tests from SymtabTest
24: [ RUN ] SymtabTest.EmptyOnOpen
24: [ OK ] SymtabTest.EmptyOnOpen (0 ms)
24: [ RUN ] SymtabTest.AddSingleEntry
24: [ OK ] SymtabTest.AddSingleEntry (0 ms)
24: [ RUN ] SymtabTest.AddTwoDistinctEntries
24: [ OK ] SymtabTest.AddTwoDistinctEntries (0 ms)
24: [ RUN ] SymtabTest.TryToAddDuplicates
24: [ OK ] SymtabTest.TryToAddDuplicates (0 ms)
24: [ RUN ] SymtabTest.AddLargeNumberOfEntries
24: [ OK ] SymtabTest.AddLargeNumberOfEntries (0 ms)
24: [ RUN ] SymtabTest.NoDuplicatesInLargeTable
24: [ OK ] SymtabTest.NoDuplicatesInLargeTable (0 ms)
24: [----------] 6 tests from SymtabTest (1 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 11 tests from 3 test cases ran. (2 ms total)
24: [ PASSED ] 11 tests.
24/54 Test #24: TopologyTest ........................ Passed 0.02 sec
test 25
Start 25: PullTest
25: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/PullTest.xml"
25: Test timeout computed to be: 30
25: [==========] Running 5 tests from 1 test case.
25: [----------] Global test environment set-up.
25: [----------] 5 tests from PullTest
25: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
25: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
25: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
25: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
25: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
25: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
25: [----------] 5 tests from PullTest (1 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 5 tests from 1 test case ran. (1 ms total)
25: [ PASSED ] 5 tests.
25/54 Test #25: PullTest ............................ Passed 0.02 sec
test 26
Start 26: AwhTest
26: Test command: /<<PKGBUILDDIR>>/build/basic/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AwhTest.xml"
26: Test timeout computed to be: 30
26: [==========] Running 12 tests from 4 test cases.
26: [----------] Global test environment set-up.
26: [----------] 1 test from BiasTest
26: [ RUN ] BiasTest.DetectsCovering
26: [ OK ] BiasTest.DetectsCovering (1 ms)
26: [----------] 1 test from BiasTest (1 ms total)
26:
26: [----------] 1 test from gridTest
26: [ RUN ] gridTest.neighborhood
26: [ OK ] gridTest.neighborhood (3 ms)
26: [----------] 1 test from gridTest (3 ms total)
26:
26: [----------] 8 tests from WithParameters/BiasTest
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (0 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (0 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (1 ms)
26: [----------] 8 tests from WithParameters/BiasTest (7 ms total)
26:
26: [----------] 2 tests from WithParameters/BiasStateTest
26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms)
26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms)
26: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 12 tests from 4 test cases ran. (12 ms total)
26: [ PASSED ] 12 tests.
26/54 Test #26: AwhTest ............................. Passed 0.03 sec
test 27
Start 27: SimdUnitTests
27: Test command: /<<PKGBUILDDIR>>/build/basic/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SimdUnitTests.xml"
27: Test timeout computed to be: 30
27: [==========] Running 86 tests from 3 test cases.
27: [----------] Global test environment set-up.
27: [----------] 41 tests from SimdScalarTest
27: [ RUN ] SimdScalarTest.load
27: [ OK ] SimdScalarTest.load (0 ms)
27: [ RUN ] SimdScalarTest.loadU
27: [ OK ] SimdScalarTest.loadU (0 ms)
27: [ RUN ] SimdScalarTest.store
27: [ OK ] SimdScalarTest.store (0 ms)
27: [ RUN ] SimdScalarTest.storeU
27: [ OK ] SimdScalarTest.storeU (0 ms)
27: [ RUN ] SimdScalarTest.setZero
27: [ OK ] SimdScalarTest.setZero (0 ms)
27: [ RUN ] SimdScalarTest.andNot
27: [ OK ] SimdScalarTest.andNot (0 ms)
27: [ RUN ] SimdScalarTest.fma
27: [ OK ] SimdScalarTest.fma (0 ms)
27: [ RUN ] SimdScalarTest.fms
27: [ OK ] SimdScalarTest.fms (0 ms)
27: [ RUN ] SimdScalarTest.fnma
27: [ OK ] SimdScalarTest.fnma (0 ms)
27: [ RUN ] SimdScalarTest.fnms
27: [ OK ] SimdScalarTest.fnms (0 ms)
27: [ RUN ] SimdScalarTest.maskAdd
27: [ OK ] SimdScalarTest.maskAdd (0 ms)
27: [ RUN ] SimdScalarTest.maskzMul
27: [ OK ] SimdScalarTest.maskzMul (0 ms)
27: [ RUN ] SimdScalarTest.maskzFma
27: [ OK ] SimdScalarTest.maskzFma (0 ms)
27: [ RUN ] SimdScalarTest.abs
27: [ OK ] SimdScalarTest.abs (0 ms)
27: [ RUN ] SimdScalarTest.max
27: [ OK ] SimdScalarTest.max (0 ms)
27: [ RUN ] SimdScalarTest.min
27: [ OK ] SimdScalarTest.min (0 ms)
27: [ RUN ] SimdScalarTest.round
27: [ OK ] SimdScalarTest.round (0 ms)
27: [ RUN ] SimdScalarTest.trunc
27: [ OK ] SimdScalarTest.trunc (0 ms)
27: [ RUN ] SimdScalarTest.reduce
27: [ OK ] SimdScalarTest.reduce (0 ms)
27: [ RUN ] SimdScalarTest.testBits
27: [ OK ] SimdScalarTest.testBits (0 ms)
27: [ RUN ] SimdScalarTest.anyTrue
27: [ OK ] SimdScalarTest.anyTrue (0 ms)
27: [ RUN ] SimdScalarTest.selectByMask
27: [ OK ] SimdScalarTest.selectByMask (0 ms)
27: [ RUN ] SimdScalarTest.selectByNotMask
27: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
27: [ RUN ] SimdScalarTest.blend
27: [ OK ] SimdScalarTest.blend (0 ms)
27: [ RUN ] SimdScalarTest.cvtR2I
27: [ OK ] SimdScalarTest.cvtR2I (0 ms)
27: [ RUN ] SimdScalarTest.cvttR2I
27: [ OK ] SimdScalarTest.cvttR2I (0 ms)
27: [ RUN ] SimdScalarTest.cvtI2R
27: [ OK ] SimdScalarTest.cvtI2R (0 ms)
27: [ RUN ] SimdScalarTest.cvtF2D
27: [ OK ] SimdScalarTest.cvtF2D (0 ms)
27: [ RUN ] SimdScalarTest.cvtD2D
27: [ OK ] SimdScalarTest.cvtD2D (0 ms)
27: [ RUN ] SimdScalarTest.loadI
27: [ OK ] SimdScalarTest.loadI (0 ms)
27: [ RUN ] SimdScalarTest.loadUI
27: [ OK ] SimdScalarTest.loadUI (0 ms)
27: [ RUN ] SimdScalarTest.storeI
27: [ OK ] SimdScalarTest.storeI (0 ms)
27: [ RUN ] SimdScalarTest.storeUI
27: [ OK ] SimdScalarTest.storeUI (0 ms)
27: [ RUN ] SimdScalarTest.andNotI
27: [ OK ] SimdScalarTest.andNotI (0 ms)
27: [ RUN ] SimdScalarTest.testBitsI
27: [ OK ] SimdScalarTest.testBitsI (0 ms)
27: [ RUN ] SimdScalarTest.selectByMaskI
27: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
27: [ RUN ] SimdScalarTest.selectByNotMaskI
27: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
27: [ RUN ] SimdScalarTest.blendI
27: [ OK ] SimdScalarTest.blendI (0 ms)
27: [ RUN ] SimdScalarTest.cvtB2IB
27: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
27: [ RUN ] SimdScalarTest.cvtIB2B
27: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
27: [ RUN ] SimdScalarTest.expandScalarsToTriplets
27: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
27: [----------] 41 tests from SimdScalarTest (2 ms total)
27:
27: [----------] 8 tests from SimdScalarUtilTest
27: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
27: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
27: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
27: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
27: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
27: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
27: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
27: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
27: [----------] 8 tests from SimdScalarUtilTest (0 ms total)
27:
27: [----------] 37 tests from SimdScalarMathTest
27: [ RUN ] SimdScalarMathTest.copysign
27: [ OK ] SimdScalarMathTest.copysign (0 ms)
27: [ RUN ] SimdScalarMathTest.invsqrtPair
27: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
27: [ RUN ] SimdScalarMathTest.inv
27: [ OK ] SimdScalarMathTest.inv (0 ms)
27: [ RUN ] SimdScalarMathTest.maskzInvsqrt
27: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
27: [ RUN ] SimdScalarMathTest.log
27: [ OK ] SimdScalarMathTest.log (0 ms)
27: [ RUN ] SimdScalarMathTest.exp2
27: [ OK ] SimdScalarMathTest.exp2 (0 ms)
27: [ RUN ] SimdScalarMathTest.exp
27: [ OK ] SimdScalarMathTest.exp (0 ms)
27: [ RUN ] SimdScalarMathTest.erf
27: [ OK ] SimdScalarMathTest.erf (0 ms)
27: [ RUN ] SimdScalarMathTest.erfc
27: [ OK ] SimdScalarMathTest.erfc (0 ms)
27: [ RUN ] SimdScalarMathTest.sincos
27: [ OK ] SimdScalarMathTest.sincos (0 ms)
27: [ RUN ] SimdScalarMathTest.sin
27: [ OK ] SimdScalarMathTest.sin (1 ms)
27: [ RUN ] SimdScalarMathTest.cos
27: [ OK ] SimdScalarMathTest.cos (0 ms)
27: [ RUN ] SimdScalarMathTest.tan
27: [ OK ] SimdScalarMathTest.tan (0 ms)
27: [ RUN ] SimdScalarMathTest.asin
27: [ OK ] SimdScalarMathTest.asin (0 ms)
27: [ RUN ] SimdScalarMathTest.acos
27: [ OK ] SimdScalarMathTest.acos (0 ms)
27: [ RUN ] SimdScalarMathTest.atan
27: [ OK ] SimdScalarMathTest.atan (0 ms)
27: [ RUN ] SimdScalarMathTest.atan2
27: [ OK ] SimdScalarMathTest.atan2 (0 ms)
27: [ RUN ] SimdScalarMathTest.pmeForceCorrection
27: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
27: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
27: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
27: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
27: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.invSingleAccuracy
27: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
27: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.logSingleAccuracy
27: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
27: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.expSingleAccuracy
27: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
27: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
27: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
27: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
27: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
27: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
27: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
27: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
27: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
27: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
27: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
27: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
27: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
27: [----------] 37 tests from SimdScalarMathTest (2 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 86 tests from 3 test cases ran. (4 ms total)
27: [ PASSED ] 86 tests.
27/54 Test #27: SimdUnitTests ....................... Passed 0.03 sec
test 28
Start 28: CompatibilityHelpersTests
28: Test command: /<<PKGBUILDDIR>>/build/basic/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml"
28: Test timeout computed to be: 30
28: [==========] Running 170 tests from 12 test cases.
28: [----------] Global test environment set-up.
28: [----------] 45 tests from OptionalTest
28: [ RUN ] OptionalTest.UnionCanContainNonPodTypes
28: [ OK ] OptionalTest.UnionCanContainNonPodTypes (0 ms)
28: [ RUN ] OptionalTest.CanDefaultConstructEmpty
28: [ OK ] OptionalTest.CanDefaultConstructEmpty (0 ms)
28: [ RUN ] OptionalTest.CanConstructFromNullopt
28: [ OK ] OptionalTest.CanConstructFromNullopt (0 ms)
28: [ RUN ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType
28: [ OK ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptional
28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptional
28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptional (1 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion
28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptional
28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting
28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptional
28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromLiteral
28: [ OK ] OptionalTest.CanCopyConstructFromLiteral (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromLiteralConverting
28: [ OK ] OptionalTest.CanCopyConstructFromLiteralConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromValue
28: [ OK ] OptionalTest.CanCopyConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromValueConverting
28: [ OK ] OptionalTest.CanCopyConstructFromValueConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromValue
28: [ OK ] OptionalTest.CanMoveConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromValueExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromValueExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting (1 ms)
28: [ RUN ] OptionalTest.CanInPlaceConstructFromLiteral
28: [ OK ] OptionalTest.CanInPlaceConstructFromLiteral (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromValue
28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromValue
28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromInitializerList
28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromInitializerList (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromInitializerList
28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromInitializerList (0 ms)
28: [ RUN ] OptionalTest.CanAssignNulloptToDisengage
28: [ OK ] OptionalTest.CanAssignNulloptToDisengage (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals
28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting
28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting
28: [ OK ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignFromLiteral
28: [ OK ] OptionalTest.CanCopyAssignFromLiteral (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignFromValue
28: [ OK ] OptionalTest.CanCopyAssignFromValue (0 ms)
28: [ RUN ] OptionalTest.CanMoveAssignFromValue
28: [ OK ] OptionalTest.CanMoveAssignFromValue (0 ms)
28: [ RUN ] OptionalTest.CanCopyEmplaceFromArguments
28: [ OK ] OptionalTest.CanCopyEmplaceFromArguments (0 ms)
28: [ RUN ] OptionalTest.CanMoveEmplaceFromArguments
28: [ OK ] OptionalTest.CanMoveEmplaceFromArguments (0 ms)
28: [ RUN ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments
28: [ OK ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments (0 ms)
28: [ RUN ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments
28: [ OK ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments (0 ms)
28: [ RUN ] OptionalTest.CanResetContent
28: [ OK ] OptionalTest.CanResetContent (0 ms)
28: [ RUN ] OptionalTest.ProvidesRelationalOperators
28: [ OK ] OptionalTest.ProvidesRelationalOperators (0 ms)
28: [ RUN ] OptionalTest.ProvidesMixedTypeRelationalOperators
28: [ OK ] OptionalTest.ProvidesMixedTypeRelationalOperators (1 ms)
28: [ RUN ] OptionalTest.CanProduceHash
28: [ OK ] OptionalTest.CanProduceHash (0 ms)
28: [ RUN ] OptionalTest.ShowAlignmentDependingOnBaseType
28: alignment_of<char>: 1
28: alignment_of<short>: 2
28: alignment_of<int>: 4
28: alignment_of<long>: 4
28: alignment_of<float>: 4
28: alignment_of<double>: 8
28: alignment_of<long double>: 8
28: alignment_of<Struct>: 1
28: [ OK ] OptionalTest.ShowAlignmentDependingOnBaseType (0 ms)
28: [ RUN ] OptionalTest.ShowSizeDependingOnBaseType
28: sizeof( nonstd::optional_lite::detail::storage_t<char> ): 1
28: sizeof( optional<char> ): 2 (1)
28: sizeof( optional<short> ): 4 (2)
28: sizeof( optional<int> ): 8 (4)
28: sizeof( optional<long> ): 8 (4)
28: sizeof( optional<float> ): 8 (4)
28: sizeof( optional<double> ): 16 (8)
28: sizeof( optional<long double> ): 16 (8)
28: sizeof( optional<Struct> ): 2 (1)
28: [ OK ] OptionalTest.ShowSizeDependingOnBaseType (0 ms)
28: [----------] 45 tests from OptionalTest (4 ms total)
28:
28: [----------] 7 tests from MakeOptionalTest
28: [ RUN ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals
28: [ OK ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals (0 ms)
28: [ RUN ] MakeOptionalTest.CanCopyConstruct
28: [ OK ] MakeOptionalTest.CanCopyConstruct (0 ms)
28: [ RUN ] MakeOptionalTest.CanMoveConstruct
28: [ OK ] MakeOptionalTest.CanMoveConstruct (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments
28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments
28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments
28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments
28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments (0 ms)
28: [----------] 7 tests from MakeOptionalTest (1 ms total)
28:
28: [----------] 4 tests from OptionalMemberSwapTest
28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged
28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged (0 ms)
28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged
28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged (0 ms)
28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged
28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged (0 ms)
28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged
28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged (0 ms)
28: [----------] 4 tests from OptionalMemberSwapTest (0 ms total)
28:
28: [----------] 4 tests from OptionalImplicitValueTest
28: [ RUN ] OptionalImplicitValueTest.CanObtainValueConst
28: [ OK ] OptionalImplicitValueTest.CanObtainValueConst (0 ms)
28: [ RUN ] OptionalImplicitValueTest.CanObtainValueNonConst
28: [ OK ] OptionalImplicitValueTest.CanObtainValueNonConst (0 ms)
28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueConst
28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueConst (0 ms)
28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst
28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst (0 ms)
28: [----------] 4 tests from OptionalImplicitValueTest (0 ms total)
28:
28: [----------] 20 tests from OptionalIntValueTest
28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst
28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst
28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst (1 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool
28: [ OK ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodConst
28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst
28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues
28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues (0 ms)
28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues
28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues (0 ms)
28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod
28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged (0 ms)
28: [----------] 20 tests from OptionalIntValueTest (2 ms total)
28:
28: [----------] 1 test from NotNullConstruction
28: [ RUN ] NotNullConstruction.Works
28: [ OK ] NotNullConstruction.Works (0 ms)
28: [----------] 1 test from NotNullConstruction (0 ms total)
28:
28: [----------] 1 test from NotNullCasting
28: [ RUN ] NotNullCasting.Works
28: [ OK ] NotNullCasting.Works (0 ms)
28: [----------] 1 test from NotNullCasting (0 ms total)
28:
28: [----------] 1 test from NotNullAssignment
28: [ RUN ] NotNullAssignment.Works
28: [ OK ] NotNullAssignment.Works (0 ms)
28: [----------] 1 test from NotNullAssignment (0 ms total)
28:
28: [----------] 1 test from MakeNotNull
28: [ RUN ] MakeNotNull.Works
28: [ OK ] MakeNotNull.Works (0 ms)
28: [----------] 1 test from MakeNotNull (0 ms total)
28:
28: [----------] 1 test from NotNull
28: [ RUN ] NotNull.WorksInContainers
28: [ OK ] NotNull.WorksInContainers (0 ms)
28: [----------] 1 test from NotNull (0 ms total)
28:
28: [----------] 80 tests from StringViewTest
28: [ RUN ] StringViewTest.CanDefaultConstructEmptyView
28: [ OK ] StringViewTest.CanDefaultConstructEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanConstructFromPointerAndSize
28: [ OK ] StringViewTest.CanConstructFromPointerAndSize (0 ms)
28: [ RUN ] StringViewTest.CanConstructFromCString
28: [ OK ] StringViewTest.CanConstructFromCString (0 ms)
28: [ RUN ] StringViewTest.CanCopyConstructFromEmptyView
28: [ OK ] StringViewTest.CanCopyConstructFromEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanCopyConstructFromNonEmptyView
28: [ OK ] StringViewTest.CanCopyConstructFromNonEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanCopyAssingFromEmptyView
28: [ OK ] StringViewTest.CanCopyAssingFromEmptyView (1 ms)
28: [ RUN ] StringViewTest.CanCopyAssingFromNonEmptyView
28: [ OK ] StringViewTest.CanCopyAssingFromNonEmptyView (0 ms)
28: [ RUN ] StringViewTest.AllowForwardIteration
28: [ OK ] StringViewTest.AllowForwardIteration (0 ms)
28: [ RUN ] StringViewTest.AllowConstForwardIteration
28: [ OK ] StringViewTest.AllowConstForwardIteration (0 ms)
28: [ RUN ] StringViewTest.AllowReverseIteration
28: [ OK ] StringViewTest.AllowReverseIteration (0 ms)
28: [ RUN ] StringViewTest.AllowConstReverseIteration
28: [ OK ] StringViewTest.AllowConstReverseIteration (0 ms)
28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaSize
28: [ OK ] StringViewTest.CanObtainSizeFromViewViaSize (0 ms)
28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaLength
28: [ OK ] StringViewTest.CanObtainSizeFromViewViaLength (0 ms)
28: [ RUN ] StringViewTest.CanObtainMaxSizeViaMaxSize
28: [ OK ] StringViewTest.CanObtainMaxSizeViaMaxSize (0 ms)
28: [ RUN ] StringViewTest.CanCheckForEmptyStringWithEmpty
28: [ OK ] StringViewTest.CanCheckForEmptyStringWithEmpty (0 ms)
28: [ RUN ] StringViewTest.CanAccessElementViaArrayIndex
28: [ OK ] StringViewTest.CanAccessElementViaArrayIndex (0 ms)
28: [ RUN ] StringViewTest.CanAccessElementViaAt
28: [ OK ] StringViewTest.CanAccessElementViaAt (0 ms)
28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsAccess
28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsAccess (0 ms)
28: [ RUN ] StringViewTest.CanAccessAllElementsViaData
28: [ OK ] StringViewTest.CanAccessAllElementsViaData (0 ms)
28: [ RUN ] StringViewTest.DataFromEmptyStringIsNullptr
28: [ OK ] StringViewTest.DataFromEmptyStringIsNullptr (0 ms)
28: [ RUN ] StringViewTest.CanRemovePrefix
28: [ OK ] StringViewTest.CanRemovePrefix (0 ms)
28: [ RUN ] StringViewTest.CanRemoveSuffix
28: [ OK ] StringViewTest.CanRemoveSuffix (0 ms)
28: [ RUN ] StringViewTest.CanSwapWithOtherView
28: [ OK ] StringViewTest.CanSwapWithOtherView (0 ms)
28: [ RUN ] StringViewTest.CanCopySubstringWithCopy
28: [ OK ] StringViewTest.CanCopySubstringWithCopy (1 ms)
28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsCopy
28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsCopy (0 ms)
28: [ RUN ] StringViewTest.CanObtainSubstringWithSubstr
28: [ OK ] StringViewTest.CanObtainSubstringWithSubstr (0 ms)
28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsSubstr
28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsSubstr (0 ms)
28: [ RUN ] StringViewTest.CanLexicallyCompareViewWithCompare
28: [ OK ] StringViewTest.CanLexicallyCompareViewWithCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareEmptyViewsWIthCompare
28: [ OK ] StringViewTest.CanCompareEmptyViewsWIthCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringWithViewViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringWithViewViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareToCStringViaCompare
28: [ OK ] StringViewTest.CanCompareToCStringViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringToCStringViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringToCStringViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCheckForPrefixViewViaStartsWith
28: [ OK ] StringViewTest.CanCheckForPrefixViewViaStartsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith
28: [ OK ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForPrefixCStringViaStartsWith
28: [ OK ] StringViewTest.CanCheckForPrefixCStringViaStartsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForSuffixViewViaEndsWith
28: [ OK ] StringViewTest.CanCheckForSuffixViewViaEndsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith
28: [ OK ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForSuffixCStringViaEndsWith
28: [ OK ] StringViewTest.CanCheckForSuffixCStringViaEndsWith (0 ms)
28: [ RUN ] StringViewTest.CanSearchForViewSubstrViaFind
28: [ OK ] StringViewTest.CanSearchForViewSubstrViaFind (0 ms)
28: [ RUN ] StringViewTest.CanSearchForCharacterViaFind
28: [ OK ] StringViewTest.CanSearchForCharacterViaFind (0 ms)
28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFind
28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFind (0 ms)
28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos
28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind
28: [ OK ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForCharacterViaFind
28: [ OK ] StringViewTest.CanBackwardsSearchForCharacterViaFind (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind
28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos
28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharacter
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharacter (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNotFoundCharacter
28: [ OK ] StringViewTest.CanSearchForFirstNotFoundCharacter (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNonMatchingCharacter
28: [ OK ] StringViewTest.CanSearchForFirstNonMatchingCharacter (1 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength
28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString
28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView
28: [ OK ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter
28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength
28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString
28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSV
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSV (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SV
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SV (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCompareToViews
28: [ OK ] StringViewTest.CanCompareToViews (0 ms)
28: [ RUN ] StringViewTest.CanCompareViewToImplicitlyConvertedView
28: [ OK ] StringViewTest.CanCompareViewToImplicitlyConvertedView (0 ms)
28: [ RUN ] StringViewTest.EmptyViewsCompareAsEqual
28: [ OK ] StringViewTest.EmptyViewsCompareAsEqual (0 ms)
28: [ RUN ] StringViewTest.CanPrintViewToPutputStream
28: [ OK ] StringViewTest.CanPrintViewToPutputStream (0 ms)
28: [ RUN ] StringViewTest.HashOfViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfViewIsEqualToHashOfString (0 ms)
28: [ RUN ] StringViewTest.HashOfWStringViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfWStringViewIsEqualToHashOfString (0 ms)
28: [ RUN ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString (0 ms)
28: [ RUN ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString (0 ms)
28: [----------] 80 tests from StringViewTest (5 ms total)
28:
28: [----------] 5 tests from StringViewExtensionTest
28: [ RUN ] StringViewExtensionTest.CanConstructViewFromString
28: [ OK ] StringViewExtensionTest.CanConstructViewFromString (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToString
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToString (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView (0 ms)
28: [----------] 5 tests from StringViewExtensionTest (0 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 170 tests from 12 test cases ran. (12 ms total)
28: [ PASSED ] 170 tests.
28/54 Test #28: CompatibilityHelpersTests ........... Passed 0.04 sec
test 29
Start 29: GmxAnaTest
29: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxAnaTest.xml"
29: Test timeout computed to be: 600
29: [==========] Running 27 tests from 5 test cases.
29: [----------] Global test environment set-up.
29: [----------] 5 tests from Entropy
29: [ RUN ] Entropy.Schlitter_300_NoLinear
29: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms)
29: [ RUN ] Entropy.Schlitter_300_Linear
29: [ OK ] Entropy.Schlitter_300_Linear (0 ms)
29: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
29: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms)
29: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
29: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms)
29: [ RUN ] Entropy.QuasiHarmonic_200_Linear
29: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms)
29: [----------] 5 tests from Entropy (1 ms total)
29:
29: [----------] 10 tests from MindistTest
29: [ RUN ] MindistTest.mindistWorksWithSingleAtoms
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.mindistWorksWithSingleAtoms (2 ms)
29: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 2: 'atom3'
29: Selected 3: 'atoms12'
29: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (3 ms)
29: [ RUN ] MindistTest.mindistDoesNotPickUpContacts
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.mindistDoesNotPickUpContacts (2 ms)
29: [ RUN ] MindistTest.mindistPicksUpContacts
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.mindistPicksUpContacts (3 ms)
29: [ RUN ] MindistTest.ngWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: Selected 2: 'atom3'
29: [ OK ] MindistTest.ngWorks (3 ms)
29: [ RUN ] MindistTest.groupWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 3: 'atoms12'
29: Selected 2: 'atom3'
29: [ OK ] MindistTest.groupWorks (2 ms)
29: [ RUN ] MindistTest.maxDistWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 2: 'atom3'
29: Selected 3: 'atoms12'
29: [ OK ] MindistTest.maxDistWorks (3 ms)
29: [ RUN ] MindistTest.noPbcWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.noPbcWorks (2 ms)
29: [ RUN ] MindistTest.resPerTimeWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 3: 'atoms12'
29: Selected 2: 'atom3'
29: [ OK ] MindistTest.resPerTimeWorks (3 ms)
29: [ RUN ] MindistTest.matrixWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 5: 'atoms123'
29: Special case: making distance matrix between all atoms in group atoms123
29: [ OK ] MindistTest.matrixWorks (2 ms)
29: [----------] 10 tests from MindistTest (25 ms total)
29:
29: [----------] 3 tests from MsdTest
29: [ RUN ] MsdTest.threeDimensionalDiffusion
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( particles) has 3 elements
29: There is one group in the index
29:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
29:
29: Used 1 restart points spaced 200 ps over 9 ps
29:
29: Fitting from 1 to 8 ps
29:
29: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
29: [ OK ] MsdTest.threeDimensionalDiffusion (3 ms)
29: [ RUN ] MsdTest.twoDimensionalDiffusion
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( particles) has 3 elements
29: There is one group in the index
29:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
29:
29: Used 1 restart points spaced 200 ps over 9 ps
29:
29: Fitting from 1 to 8 ps
29:
29: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
29: [ OK ] MsdTest.twoDimensionalDiffusion (3 ms)
29: [ RUN ] MsdTest.oneDimensionalDiffusion
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( particles) has 3 elements
29: There is one group in the index
29:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
29:
29: Used 1 restart points spaced 200 ps over 9 ps
29:
29: Fitting from 1 to 8 ps
29:
29: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
29: [ OK ] MsdTest.oneDimensionalDiffusion (3 ms)
29: [----------] 3 tests from MsdTest (9 ms total)
29:
29: [----------] 3 tests from MsdMolTest
29: [ RUN ] MsdMolTest.diffMolMassWeighted
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
29: For a correct single-point energy evaluation with nsteps = 0, use
29: continuation = yes to avoid constraining the input coordinates.
29:
29: Setting the LD random seed to -819691689
29: Generated 330891 of the 330891 non-bonded parameter combinations
29: Generating 1-4 interactions: fudge = 0.5
29: Generated 330891 of the 330891 1-4 parameter combinations
29: Excluding 2 bonded neighbours molecule type 'SOL'
29: Number of degrees of freedom in T-Coupling group rest is 27.00
29:
29: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
29: NVE simulation with an initial temperature of zero: will use a Verlet
29: buffer of 10%. Check your energy drift!
29:
29:
29: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
29: You are using a plain Coulomb cut-off, which might produce artifacts.
29: You might want to consider using PME electrostatics.
29:
29:
29:
29: There were 3 notes
29: Calculating diffusion coefficients for molecules.
29: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
29: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( water) has 15 elements
29: There is one group in the index
29: Split group of 15 atoms into 5 molecules
29: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
29:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
29:
29: Used 1 restart points spaced 200 ps over 0.1 ps
29:
29: This run will generate roughly 0 Mb of data
29: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
29: Fitting from 0.008 to 0.088 ps
29:
29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
29: [ OK ] MsdMolTest.diffMolMassWeighted (860 ms)
29: [ RUN ] MsdMolTest.diffMolNonMassWeighted
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
29: For a correct single-point energy evaluation with nsteps = 0, use
29: continuation = yes to avoid constraining the input coordinates.
29:
29: Setting the LD random seed to -755304697
29: Generated 330891 of the 330891 non-bonded parameter combinations
29: Generating 1-4 interactions: fudge = 0.5
29: Generated 330891 of the 330891 1-4 parameter combinations
29: Excluding 2 bonded neighbours molecule type 'SOL'
29: Number of degrees of freedom in T-Coupling group rest is 27.00
29:
29: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
29: NVE simulation with an initial temperature of zero: will use a Verlet
29: buffer of 10%. Check your energy drift!
29:
29:
29: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
29: You are using a plain Coulomb cut-off, which might produce artifacts.
29: You might want to consider using PME electrostatics.
29:
29:
29:
29: There were 3 notes
29: Calculating diffusion coefficients for molecules.
29: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
29: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( water) has 15 elements
29: There is one group in the index
29: Split group of 15 atoms into 5 molecules
29: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
29:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
29:
29: Used 1 restart points spaced 200 ps over 0.1 ps
29:
29: This run will generate roughly 0 Mb of data
29: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
29: Fitting from 0.008 to 0.088 ps
29:
29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
29: [ OK ] MsdMolTest.diffMolNonMassWeighted (854 ms)
29: [ RUN ] MsdMolTest.diffMolSelected
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
29: For a correct single-point energy evaluation with nsteps = 0, use
29: continuation = yes to avoid constraining the input coordinates.
29:
29: Setting the LD random seed to 792009920
29: Generated 330891 of the 330891 non-bonded parameter combinations
29: Generating 1-4 interactions: fudge = 0.5
29: Generated 330891 of the 330891 1-4 parameter combinations
29: Excluding 2 bonded neighbours molecule type 'SOL'
29: Number of degrees of freedom in T-Coupling group rest is 27.00
29:
29: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
29: NVE simulation with an initial temperature of zero: will use a Verlet
29: buffer of 10%. Check your energy drift!
29:
29:
29: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
29: You are using a plain Coulomb cut-off, which might produce artifacts.
29: You might want to consider using PME electrostatics.
29:
29:
29:
29: There were 3 notes
29: Calculating diffusion coefficients for molecules.
29: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
29: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( mol) has 9 elements
29: There is one group in the index
29: Split group of 9 atoms into 3 molecules
29: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
29:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
29:
29: Used 1 restart points spaced 200 ps over 0.1 ps
29:
29: This run will generate roughly 0 Mb of data
29: <D> = 7.3593 Std. Dev. = 9.7910 Error = 5.6529
29: Fitting from 0.008 to 0.088 ps
29:
29: D[ mol] 7.8614 (+/- 1.5618) 1e-5 cm^2/s
29: [ OK ] MsdMolTest.diffMolSelected (852 ms)
29: [----------] 3 tests from MsdMolTest (2566 ms total)
29:
29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group: trr version: GMX_trn_file (single precision)
29:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (4 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (5 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (4 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group: Reading frames from gro file '', 6 atoms.
29:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (3 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
29:
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (4 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (3 ms)
29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (23 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 27 tests from 5 test cases ran. (2625 ms total)
29: [ PASSED ] 27 tests.
29/54 Test #29: GmxAnaTest .......................... Passed 2.65 sec
test 30
Start 30: GmxPreprocessTests
30: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxPreprocessTests.xml"
30: Test timeout computed to be: 30
30: [==========] Running 69 tests from 10 test cases.
30: [----------] Global test environment set-up.
30: [----------] 4 tests from GenconfTest
30: [ RUN ] GenconfTest.nbox_Works
30: [ OK ] GenconfTest.nbox_Works (2 ms)
30: [ RUN ] GenconfTest.nbox_norenumber_Works
30: [ OK ] GenconfTest.nbox_norenumber_Works (1 ms)
30: [ RUN ] GenconfTest.nbox_dist_Works
30: [ OK ] GenconfTest.nbox_dist_Works (2 ms)
30: [ RUN ] GenconfTest.nbox_rot_Works
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: [ OK ] GenconfTest.nbox_rot_Works (3 ms)
30: [----------] 4 tests from GenconfTest (8 ms total)
30:
30: [----------] 2 tests from GenionTest
30: [ RUN ] GenionTest.HighConcentrationIonPlacement
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
30: buffer. The cluster pair list does have a buffering effect, but choosing
30: a larger rlist might be necessary for good energy conservation.
30:
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to 1289851432
30: Generated 331705 of the 331705 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 331705 of the 331705 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Excluding 3 bonded neighbours molecule type 'methane'
30: Number of degrees of freedom in T-Coupling group rest is 1308.00
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
30: Group 0 ( System) has 653 elements
30: Group 1 ( Water) has 648 elements
30: Group 2 ( SOL) has 648 elements
30: Group 3 ( non-Water) has 5 elements
30: Group 4 ( Other) has 5 elements
30: Group 5 ( METH) has 5 elements
30: Select a group: Number of (3-atomic) solvent molecules: 216
30: Using random seed 1997.
30: Replacing solvent molecule 56 (atom 168) with NA
30: Replacing solvent molecule 120 (atom 360) with NA
30: Replacing solvent molecule 182 (atom 546) with NA
30: Replacing solvent molecule 71 (atom 213) with NA
30: Replacing solvent molecule 189 (atom 567) with CL
30: Replacing solvent molecule 54 (atom 162) with CL
30: Replacing solvent molecule 155 (atom 465) with CL
30: Replacing solvent molecule 99 (atom 297) with CL
30:
30: Analysing residue names:
30: There are: 216 Water residues
30: There are: 1 Other residues
30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
30: This run will generate roughly 0 Mb of data
30: Will try to add 4 NA ions and 4 CL ions.
30: Select a continuous group of solvent molecules
30: Selected 1: 'Water'
30: [ OK ] GenionTest.HighConcentrationIonPlacement (866 ms)
30: [ RUN ] GenionTest.NoIonPlacement
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
30: buffer. The cluster pair list does have a buffering effect, but choosing
30: a larger rlist might be necessary for good energy conservation.
30:
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to 1986430009
30: Generated 331705 of the 331705 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 331705 of the 331705 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Excluding 3 bonded neighbours molecule type 'methane'
30: Number of degrees of freedom in T-Coupling group rest is 1308.00
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
30: No ions to add, will just copy input configuration.
30: Analysing residue names:
30: There are: 216 Water residues
30: There are: 1 Other residues
30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
30: This run will generate roughly 0 Mb of data
30: [ OK ] GenionTest.NoIonPlacement (853 ms)
30: [----------] 2 tests from GenionTest (1719 ms total)
30:
30: [----------] 1 test from GenRestrTest
30: [ RUN ] GenRestrTest.SimpleRestraintsGenerated
30:
30: Reading structure file
30: Group 0 ( System) has 156 elements
30: Group 1 ( Protein) has 156 elements
30: Group 2 ( Protein-H) has 75 elements
30: Group 3 ( C-alpha) has 10 elements
30: Group 4 ( Backbone) has 30 elements
30: Group 5 ( MainChain) has 40 elements
30: Group 6 ( MainChain+Cb) has 49 elements
30: Group 7 ( MainChain+H) has 52 elements
30: Group 8 ( SideChain) has 104 elements
30: Group 9 ( SideChain-H) has 35 elements
30: Select a group: Select group to position restrain
30: Selected 3: 'C-alpha'
30: [ OK ] GenRestrTest.SimpleRestraintsGenerated (5 ms)
30: [----------] 1 test from GenRestrTest (5 ms total)
30:
30: [----------] 9 tests from PreprocessingAtomTypesTest
30: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate
30: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid
30: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks
30: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks
30: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry
30: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound
30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound
30: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber
30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber
30: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms)
30: [----------] 9 tests from PreprocessingAtomTypesTest (1 ms total)
30:
30: [----------] 10 tests from PreprocessingBondAtomTypeTest
30: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate
30: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid
30: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks
30: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks
30: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry
30: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType
30: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound
30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound
30: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber
30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber
30: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms)
30: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total)
30:
30: [----------] 5 tests from InsertMoleculesTest
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
30: Reading solute configuration
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 8 atoms)!
30:
30: Added 1 molecules (out of 1 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
30:
30: Output configuration contains 8 atoms in 4 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (4 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 2 atoms)!
30:
Try 2 success (now 4 atoms)!
30:
Try 3 success (now 6 atoms)!
30:
Try 4 success (now 8 atoms)!
30:
Try 5 success (now 10 atoms)!
30:
30: Added 5 molecules (out of 5 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
30:
30: Output configuration contains 10 atoms in 10 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (4 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
30: Reading solute configuration
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 8 atoms)!
30:
Try 2 success (now 10 atoms)!
30:
30: Added 2 molecules (out of 2 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
30:
30: Output configuration contains 10 atoms in 4 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (3 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
30: Reading solute configuration
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 650 atoms)!
30:
Try 2 success (now 652 atoms)!
30:
Try 3 success (now 654 atoms)!
30:
Try 4 success (now 656 atoms)!
30:
30: Added 4 molecules (out of 4 requested)
30: Replaced 8 residues (24 atoms)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
30:
30: Output configuration contains 632 atoms in 212 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (18 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
30:
30:
Try 1 success (now 2 atoms)!
30:
Try 2 success (now 4 atoms)!
30:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
30:
Try 13 success (now 6 atoms)!
30:
30: Added 3 molecules (out of 4 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
30:
30: Output configuration contains 6 atoms in 3 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (4 ms)
30: [----------] 5 tests from InsertMoleculesTest (35 ms total)
30:
30: [----------] 14 tests from GetIrTest
30: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
30: Ignoring obsolete mdp entry 'title'
30: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (9 ms)
30: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals
30: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (9 ms)
30: [ RUN ] GetIrTest.AcceptsKeyWithoutValue
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsKeyWithoutValue (7 ms)
30: [ RUN ] GetIrTest.RejectsValueWithoutKey
30: [ OK ] GetIrTest.RejectsValueWithoutKey (9 ms)
30: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue
30: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (8 ms)
30: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (7 ms)
30: [ RUN ] GetIrTest.AcceptsEmptyLines
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsEmptyLines (7 ms)
30: [ RUN ] GetIrTest.AcceptsElectricField
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsElectricField (7 ms)
30: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (7 ms)
30: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (7 ms)
30: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys
30: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (2 ms)
30: [ RUN ] GetIrTest.AcceptsImplicitSolventNo
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsImplicitSolventNo (7 ms)
30: [ RUN ] GetIrTest.RejectsImplicitSolventYes
30: [ OK ] GetIrTest.RejectsImplicitSolventYes (9 ms)
30: [ RUN ] GetIrTest.AcceptsMimic
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsMimic (7 ms)
30: [----------] 14 tests from GetIrTest (102 ms total)
30:
30: [----------] 5 tests from SolvateTest
30: [ RUN ] SolvateTest.cs_box_Works
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 1x1x1 boxes
30: Solvent box contains 270 atoms in 90 residues
30: Removed 129 solvent atoms due to solvent-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 47 residues
30: Generated solvent containing 141 atoms in 47 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
30:
30: Output configuration contains 141 atoms in 47 residues
30: Volume : 1.331 (nm^3)
30: Density : 1056.36 (g/l)
30: Number of solvent molecules: 47
30:
30: [ OK ] SolvateTest.cs_box_Works (19 ms)
30: [ RUN ] SolvateTest.cs_cp_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 2x2x2 boxes
30: Solvent box contains 3660 atoms in 1220 residues
30: Removed 987 solvent atoms due to solvent-solvent overlap
30: Removed 15 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 886 residues
30: Generated solvent containing 2658 atoms in 886 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
30:
30: Output configuration contains 2664 atoms in 888 residues
30: Volume : 27.2709 (nm^3)
30: Density : 974.777 (g/l)
30: Number of solvent molecules: 886
30:
30: [ OK ] SolvateTest.cs_cp_Works (99 ms)
30: [ RUN ] SolvateTest.cs_cp_p_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 2x2x2 boxes
30: Solvent box contains 3660 atoms in 1220 residues
30: Removed 987 solvent atoms due to solvent-solvent overlap
30: Removed 15 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 886 residues
30: Generated solvent containing 2658 atoms in 886 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
30:
30: Output configuration contains 2664 atoms in 888 residues
30: Volume : 27.2709 (nm^3)
30: Density : 974.777 (g/l)
30: Number of solvent molecules: 886
30:
30: Processing topology
30: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top)
30: [ OK ] SolvateTest.cs_cp_p_Works (100 ms)
30: [ RUN ] SolvateTest.shell_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 2x2x2 boxes
30: Solvent box contains 3660 atoms in 1220 residues
30: Removed 987 solvent atoms due to solvent-solvent overlap
30: Removed 1902 solvent atoms more than 1.000000 nm from solute.
30: Removed 15 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 252 residues
30: Generated solvent containing 756 atoms in 252 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
30:
30: Output configuration contains 762 atoms in 254 residues
30: Volume : 27.2709 (nm^3)
30: Density : 279.3 (g/l)
30: Number of solvent molecules: 252
30:
30: [ OK ] SolvateTest.shell_Works (47 ms)
30: [ RUN ] SolvateTest.update_Topology_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 3x3x3 boxes
30: Solvent box contains 14952 atoms in 4984 residues
30: Removed 2787 solvent atoms due to solvent-solvent overlap
30: Removed 30 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 2 different molecule types:
30: HOH ( 3 atoms): 1876 residues
30: SOL ( 3 atoms): 2169 residues
30: Generated solvent containing 0 atoms in 0 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
30:
30: Output configuration contains 12141 atoms in 4047 residues
30: Volume : 125 (nm^3)
30: Density : 968.963 (g/l)
30: Number of solvent molecules: 4045
30:
30: Processing topology
30: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
30: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
30: [ OK ] SolvateTest.update_Topology_Works (397 ms)
30: [----------] 5 tests from SolvateTest (662 ms total)
30:
30: [----------] 1 test from TopDirTests
30: [ RUN ] TopDirTests.NamesArrayHasCorrectSize
30: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms)
30: [----------] 1 test from TopDirTests (0 ms total)
30:
30: [----------] 18 tests from SinglePeptideFragments/EditconfTest
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (15 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (13 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (13 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (9 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (6 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (6 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (10 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (7 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (7 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (13 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (12 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (12 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (6 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (4 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (4 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (7 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (5 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (6 ms)
30: [----------] 18 tests from SinglePeptideFragments/EditconfTest (157 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 69 tests from 10 test cases ran. (2691 ms total)
30: [ PASSED ] 69 tests.
30/54 Test #30: GmxPreprocessTests .................. Passed 2.72 sec
test 31
Start 31: Pdb2gmx1Test
31: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx1Test.xml"
31: Test timeout computed to be: 30
31: [==========] Running 24 tests from 1 test case.
31: [----------] Global test environment set-up.
31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 0 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (180 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 0 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (199 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 0 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (183 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 0 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (167 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Marked 124 virtual sites
31: Added 16 dummy masses
31: Added 26 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 130 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (192 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Marked 132 virtual sites
31: Added 10 dummy masses
31: Added 19 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 133 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (211 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Marked 123 virtual sites
31: Added 22 dummy masses
31: Added 35 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 132 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (199 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Marked 111 virtual sites
31: Added 18 dummy masses
31: Added 31 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 116 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (179 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 0 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (179 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 0 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (199 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 0 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (182 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 0 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (165 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Marked 124 virtual sites
31: Added 16 dummy masses
31: Added 26 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 130 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (192 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Marked 132 virtual sites
31: Added 10 dummy masses
31: Added 19 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 133 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (210 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Marked 123 virtual sites
31: Added 22 dummy masses
31: Added 35 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 132 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (198 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Marked 111 virtual sites
31: Added 18 dummy masses
31: Added 31 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 116 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (179 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 0 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (177 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 0 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (199 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 0 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (181 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 0 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (166 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Marked 124 virtual sites
31: Added 16 dummy masses
31: Added 26 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 130 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (191 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Marked 132 virtual sites
31: Added 10 dummy masses
31: Added 19 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 133 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (210 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Marked 123 virtual sites
31: Added 22 dummy masses
31: Added 35 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 132 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (198 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Marked 111 virtual sites
31: Added 18 dummy masses
31: Added 31 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 116 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (179 ms)
31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (4517 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 24 tests from 1 test case ran. (4517 ms total)
31: [ PASSED ] 24 tests.
31/54 Test #31: Pdb2gmx1Test ........................ Passed 4.54 sec
test 32
Start 32: Pdb2gmx2Test
32: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx2Test.xml"
32: Test timeout computed to be: 30
32: [==========] Running 32 tests from 2 test cases.
32: [----------] Global test environment set-up.
32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (130 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (146 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (129 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (121 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Marked 37 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 37 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (131 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Marked 53 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 51 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (151 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Marked 36 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 36 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (134 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Marked 33 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 31 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (126 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (126 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (144 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (129 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (120 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Marked 37 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 37 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (131 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Marked 53 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 51 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (149 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Marked 36 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 36 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (132 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Marked 33 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 31 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (124 ms)
32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (2127 ms total)
32:
32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (138 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (158 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (140 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (133 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Marked 39 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 39 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (143 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Marked 57 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 55 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (163 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Marked 38 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 38 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (145 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Marked 35 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 33 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (137 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (137 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (157 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (140 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (132 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Marked 39 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 39 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (142 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Marked 57 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 55 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (163 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Marked 38 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 38 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (145 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Marked 35 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 33 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (137 ms)
32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (2312 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 32 tests from 2 test cases ran. (4439 ms total)
32: [ PASSED ] 32 tests.
32/54 Test #32: Pdb2gmx2Test ........................ Passed 4.46 sec
test 33
Start 33: Pdb2gmx3Test
33: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx3Test.xml"
33: Test timeout computed to be: 30
33: [==========] Running 28 tests from 4 test cases.
33: [----------] Global test environment set-up.
33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 255, now 254
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 691 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 691 dihedrals, 51 impropers, 457 angles
33: 650 pairs, 254 bonds and 0 virtual sites
33: Total mass 1846.132 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (174 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 291, now 290
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 788 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 788 dihedrals, 72 impropers, 516 angles
33: 736 pairs, 290 bonds and 0 virtual sites
33: Total mass 2088.366 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (192 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 262, now 261
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 727 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 727 dihedrals, 56 impropers, 472 angles
33: 667 pairs, 261 bonds and 0 virtual sites
33: Total mass 1861.124 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (177 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 233, now 232
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 634 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 634 dihedrals, 48 impropers, 419 angles
33: 597 pairs, 232 bonds and 0 virtual sites
33: Total mass 1662.888 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (159 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 255, now 254
33: Marked 124 virtual sites
33: Added 16 dummy masses
33: Added 26 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 691 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 691 dihedrals, 51 impropers, 457 angles
33: 650 pairs, 254 bonds and 130 virtual sites
33: Total mass 1846.132 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (186 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 291, now 290
33: Marked 132 virtual sites
33: Added 10 dummy masses
33: Added 19 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 788 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 788 dihedrals, 72 impropers, 516 angles
33: 736 pairs, 290 bonds and 133 virtual sites
33: Total mass 2088.366 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (206 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 262, now 261
33: Marked 123 virtual sites
33: Added 22 dummy masses
33: Added 35 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 727 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 727 dihedrals, 56 impropers, 472 angles
33: 667 pairs, 261 bonds and 132 virtual sites
33: Total mass 1861.124 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (191 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 233, now 232
33: Marked 111 virtual sites
33: Added 18 dummy masses
33: Added 31 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 634 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 634 dihedrals, 48 impropers, 419 angles
33: 597 pairs, 232 bonds and 116 virtual sites
33: Total mass 1662.888 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (170 ms)
33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (1455 ms total)
33:
33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 254, now 254
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 663 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 663 dihedrals, 48 impropers, 457 angles
33: 650 pairs, 254 bonds and 0 virtual sites
33: Total mass 1846.115 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (164 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 290, now 290
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 778 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 778 dihedrals, 49 impropers, 516 angles
33: 736 pairs, 290 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (184 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 261, now 261
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 696 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 696 dihedrals, 39 impropers, 472 angles
33: 667 pairs, 261 bonds and 0 virtual sites
33: Total mass 1861.130 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (167 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 232, now 232
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 618 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 618 dihedrals, 38 impropers, 419 angles
33: 597 pairs, 232 bonds and 0 virtual sites
33: Total mass 1662.885 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (151 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 254, now 254
33: Marked 124 virtual sites
33: Added 16 dummy masses
33: Added 26 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 663 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 663 dihedrals, 48 impropers, 457 angles
33: 650 pairs, 254 bonds and 130 virtual sites
33: Total mass 1846.115 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (176 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 290, now 290
33: Marked 132 virtual sites
33: Added 10 dummy masses
33: Added 19 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 778 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 778 dihedrals, 49 impropers, 516 angles
33: 736 pairs, 290 bonds and 133 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (195 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 261, now 261
33: Marked 123 virtual sites
33: Added 22 dummy masses
33: Added 35 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 696 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 696 dihedrals, 39 impropers, 472 angles
33: 667 pairs, 261 bonds and 132 virtual sites
33: Total mass 1861.130 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (184 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 232, now 232
33: Marked 111 virtual sites
33: Added 18 dummy masses
33: Added 31 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 618 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 618 dihedrals, 38 impropers, 419 angles
33: 597 pairs, 232 bonds and 116 virtual sites
33: Total mass 1662.885 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (164 ms)
33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (1386 ms total)
33:
33: [----------] 8 tests from ChainSep/Pdb2gmxTest
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 258, now 258
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 651 pairs
33: Before cleaning: 661 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 10 cmap torsion pairs
33: There are 661 dihedrals, 46 impropers, 463 angles
33: 648 pairs, 258 bonds and 0 virtual sites
33: Total mass 1882.146 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on changing chain id only (ignoring TER records).
33:
33: Merged chains into joint molecule definitions at 2 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Identified residue PHE6 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Start terminus PHE-6: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 258 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (166 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 50, now 50
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 123 pairs
33: Before cleaning: 123 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 2 cmap torsion pairs
33: There are 123 dihedrals, 9 impropers, 88 angles
33: 123 pairs, 50 bonds and 0 virtual sites
33: Total mass 434.421 a.m.u.
33: Total charge -2.000 e
33: Writing topology
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 10 donors and 7 acceptors were found.
33: There are 7 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS8
33: NE223
33: MET12 SD55 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 125, now 125
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 317 pairs
33: Before cleaning: 322 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 5 cmap torsion pairs
33: There are 322 dihedrals, 19 impropers, 227 angles
33: 314 pairs, 125 bonds and 0 virtual sites
33: Total mass 846.083 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 258 atoms and 16 residues
33: Total mass in system 1882.146 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on changing chain id only (ignoring TER records).
33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 4 28
33: 2 'B' 7 58
33: 3 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (28 atoms, 4 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 4 residues with 51 atoms
33: Chain time...
33: Processing chain 2 'B' (58 atoms, 7 residues)
33: Identified residue PHE6 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus PHE-6: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 7 residues with 124 atoms
33: Chain time...
33: Processing chain 3 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 51 atoms 4 residues
33: Including chain 2 in system: 124 atoms 7 residues
33: Including chain 3 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (124 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 258, now 258
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 651 pairs
33: Before cleaning: 661 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 10 cmap torsion pairs
33: There are 661 dihedrals, 46 impropers, 463 angles
33: 648 pairs, 258 bonds and 0 virtual sites
33: Total mass 1882.146 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records only (ignoring chain id).
33:
33: Merged chains into joint molecule definitions at 2 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ILE-9: COO-
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 258 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (167 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 10 donors and 12 acceptors were found.
33: There are 13 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3
33: SG9
33: HIS8 NE251 1.055
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 115, now 115
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 288 pairs
33: Before cleaning: 293 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 6 cmap torsion pairs
33: There are 293 dihedrals, 23 impropers, 203 angles
33: 285 pairs, 115 bonds and 0 virtual sites
33: Total mass 888.952 a.m.u.
33: Total charge -2.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 60, now 60
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 152 pairs
33: Before cleaning: 152 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 152 dihedrals, 5 impropers, 112 angles
33: 152 pairs, 60 bonds and 0 virtual sites
33: Total mass 391.552 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 258 atoms and 16 residues
33: Total mass in system 1882.146 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records only (ignoring chain id).
33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 8 61
33: 2 'B' 3 25
33: 3 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (61 atoms, 8 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ILE-9: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 8 residues with 114 atoms
33: Chain time...
33: Processing chain 2 'B' (25 atoms, 3 residues)
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 61 atoms
33: Chain time...
33: Processing chain 3 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 114 atoms 8 residues
33: Including chain 2 in system: 61 atoms 3 residues
33: Including chain 3 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (123 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 260, now 260
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 650 pairs
33: Before cleaning: 660 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 8 cmap torsion pairs
33: There are 660 dihedrals, 45 impropers, 466 angles
33: 647 pairs, 260 bonds and 0 virtual sites
33: Total mass 1900.162 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33:
33: Merged chains into joint molecule definitions at 3 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Identified residue PHE6 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Start terminus PHE-6: NH3+
33: End terminus ILE-9: COO-
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 261 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (168 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 50, now 50
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 123 pairs
33: Before cleaning: 123 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 2 cmap torsion pairs
33: There are 123 dihedrals, 9 impropers, 88 angles
33: 123 pairs, 50 bonds and 0 virtual sites
33: Total mass 434.421 a.m.u.
33: Total charge -2.000 e
33: Writing topology
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 6 donors and 4 acceptors were found.
33: There are 3 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 67, now 67
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 164 pairs
33: Before cleaning: 169 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 2 cmap torsion pairs
33: There are 169 dihedrals, 13 impropers, 118 angles
33: 161 pairs, 67 bonds and 0 virtual sites
33: Total mass 472.547 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 60, now 60
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 152 pairs
33: Before cleaning: 152 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 152 dihedrals, 5 impropers, 112 angles
33: 152 pairs, 60 bonds and 0 virtual sites
33: Total mass 391.552 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 261 atoms and 16 residues
33: Total mass in system 1900.162 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: WARNING: Chain identifier 'B' is used in two non-sequential blocks.
33: They will be treated as separate chains unless you reorder your file.
33: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 4 28
33: 2 'B' 4 33
33: 3 'B' 3 25
33: 4 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (28 atoms, 4 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 4 residues with 51 atoms
33: Chain time...
33: Processing chain 2 'B' (33 atoms, 4 residues)
33: Identified residue PHE6 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Start terminus PHE-6: NH3+
33: End terminus ILE-9: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 4 residues with 66 atoms
33: Chain time...
33: Processing chain 3 'B' (25 atoms, 3 residues)
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 61 atoms
33: Chain time...
33: Processing chain 4 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 51 atoms 4 residues
33: Including chain 2 in system: 66 atoms 4 residues
33: Including chain 3 in system: 61 atoms 3 residues
33: Including chain 4 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (123 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 256, now 256
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 652 pairs
33: Before cleaning: 662 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 12 cmap torsion pairs
33: There are 662 dihedrals, 47 impropers, 460 angles
33: 649 pairs, 256 bonds and 0 virtual sites
33: Total mass 1864.131 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records and chain id changing.
33:
33: Merged chains into joint molecule definitions at 1 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (165 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 14 donors and 15 acceptors were found.
33: There are 20 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 173, now 173
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 441 pairs
33: Before cleaning: 446 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 9 cmap torsion pairs
33: There are 446 dihedrals, 29 impropers, 312 angles
33: 438 pairs, 173 bonds and 0 virtual sites
33: Total mass 1262.488 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 255 atoms and 16 residues
33: Total mass in system 1864.131 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records and chain id changing.
33: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 11 86
33: 2 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (86 atoms, 11 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 11 residues with 172 atoms
33: Chain time...
33: Processing chain 2 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 172 atoms 11 residues
33: Including chain 2 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (126 ms)
33: [----------] 8 tests from ChainSep/Pdb2gmxTest (1162 ms total)
33:
33: [----------] 4 tests from ChainChanges/Pdb2gmxTest
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on changing chain id only (ignoring TER records).
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (83 ms)
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records only (ignoring chain id).
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (82 ms)
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (83 ms)
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records and chain id changing.
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (82 ms)
33: [----------] 4 tests from ChainChanges/Pdb2gmxTest (330 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 28 tests from 4 test cases ran. (4333 ms total)
33: [ PASSED ] 28 tests.
33/54 Test #33: Pdb2gmx3Test ........................ Passed 4.36 sec
test 34
Start 34: CorrelationsTest
34: Test command: /<<PKGBUILDDIR>>/build/basic/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CorrelationsTest.xml"
34: Test timeout computed to be: 30
34: [==========] Running 21 tests from 3 test cases.
34: [----------] Global test environment set-up.
34: [----------] 10 tests from AutocorrTest
34: [ RUN ] AutocorrTest.EacNormal
34: [ OK ] AutocorrTest.EacNormal (22 ms)
34: [ RUN ] AutocorrTest.EacNoNormalize
34: [ OK ] AutocorrTest.EacNoNormalize (16 ms)
34: [ RUN ] AutocorrTest.EacCos
34: [ OK ] AutocorrTest.EacCos (29 ms)
34: [ RUN ] AutocorrTest.EacVector
34: [ OK ] AutocorrTest.EacVector (44 ms)
34: [ RUN ] AutocorrTest.EacRcross
34: [ OK ] AutocorrTest.EacRcross (3 ms)
34: [ RUN ] AutocorrTest.EacP0
34: [ OK ] AutocorrTest.EacP0 (43 ms)
34: [ RUN ] AutocorrTest.EacP1
34: [ OK ] AutocorrTest.EacP1 (42 ms)
34: [ RUN ] AutocorrTest.EacP2
34: [ OK ] AutocorrTest.EacP2 (83 ms)
34: [ RUN ] AutocorrTest.EacP3
34: [ OK ] AutocorrTest.EacP3 (9 ms)
34: [ RUN ] AutocorrTest.EacP4
34: [ OK ] AutocorrTest.EacP4 (44 ms)
34: [----------] 10 tests from AutocorrTest (344 ms total)
34:
34: [----------] 1 test from ManyAutocorrelationTest
34: [ RUN ] ManyAutocorrelationTest.Empty
34: [ OK ] ManyAutocorrelationTest.Empty (0 ms)
34: [----------] 1 test from ManyAutocorrelationTest (0 ms total)
34:
34: [----------] 10 tests from ExpfitTest
34: [ RUN ] ExpfitTest.EffnEXP1
34: [ OK ] ExpfitTest.EffnEXP1 (2 ms)
34: [ RUN ] ExpfitTest.EffnEXP2
34: [ OK ] ExpfitTest.EffnEXP2 (2 ms)
34: [ RUN ] ExpfitTest.EffnEXPEXP
34: [ OK ] ExpfitTest.EffnEXPEXP (5 ms)
34: [ RUN ] ExpfitTest.EffnEXP5
34: [ OK ] ExpfitTest.EffnEXP5 (13 ms)
34: [ RUN ] ExpfitTest.EffnEXP7
34: [ OK ] ExpfitTest.EffnEXP7 (9 ms)
34: [ RUN ] ExpfitTest.EffnEXP9
34: [ OK ] ExpfitTest.EffnEXP9 (70 ms)
34: [ RUN ] ExpfitTest.EffnERF
34: [ OK ] ExpfitTest.EffnERF (7 ms)
34: [ RUN ] ExpfitTest.EffnERREST
34: [ OK ] ExpfitTest.EffnERREST (3 ms)
34: [ RUN ] ExpfitTest.EffnVAC
34: [ OK ] ExpfitTest.EffnVAC (14 ms)
34: [ RUN ] ExpfitTest.EffnPRES
34: [ OK ] ExpfitTest.EffnPRES (39 ms)
34: [----------] 10 tests from ExpfitTest (165 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 21 tests from 3 test cases ran. (542 ms total)
34: [ PASSED ] 21 tests.
34/54 Test #34: CorrelationsTest .................... Passed 0.56 sec
test 35
Start 35: AnalysisDataUnitTests
35: Test command: /<<PKGBUILDDIR>>/build/basic/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml"
35: Test timeout computed to be: 30
35: [==========] Running 69 tests from 14 test cases.
35: [----------] Global test environment set-up.
35: [----------] 3 tests from AnalysisDataInitializationTest
35: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
35: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms)
35: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
35: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms)
35: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
35: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms)
35: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (3 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (5 ms)
35: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (2 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (1 ms)
35: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (1 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/0 (25 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
35: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (3 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (2 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/1 (30 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (8 ms)
35: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (2 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (3 ms)
35: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (2 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/2 (35 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (6 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (8 ms)
35: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (2 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (3 ms)
35: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (2 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/3 (35 ms total)
35:
35: [----------] 4 tests from AnalysisArrayDataTest
35: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
35: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisArrayDataTest.StorageWorks
35: [ OK ] AnalysisArrayDataTest.StorageWorks (2 ms)
35: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
35: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms)
35: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
35: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
35: [----------] 4 tests from AnalysisArrayDataTest (6 ms total)
35:
35: [----------] 6 tests from AverageModuleTest
35: [ RUN ] AverageModuleTest.BasicTest
35: [ OK ] AverageModuleTest.BasicTest (4 ms)
35: [ RUN ] AverageModuleTest.HandlesMultipointData
35: [ OK ] AverageModuleTest.HandlesMultipointData (4 ms)
35: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
35: [ OK ] AverageModuleTest.HandlesMultipleDataSets (5 ms)
35: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
35: [ OK ] AverageModuleTest.HandlesDataSetAveraging (5 ms)
35: [ RUN ] AverageModuleTest.CanCustomizeXAxis
35: [ OK ] AverageModuleTest.CanCustomizeXAxis (4 ms)
35: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
35: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (4 ms)
35: [----------] 6 tests from AverageModuleTest (28 ms total)
35:
35: [----------] 2 tests from FrameAverageModuleTest
35: [ RUN ] FrameAverageModuleTest.BasicTest
35: [ OK ] FrameAverageModuleTest.BasicTest (4 ms)
35: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
35: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (5 ms)
35: [----------] 2 tests from FrameAverageModuleTest (9 ms total)
35:
35: [----------] 7 tests from AnalysisHistogramSettingsTest
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
35: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total)
35:
35: [----------] 2 tests from SimpleHistogramModuleTest
35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (6 ms)
35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (6 ms)
35: [----------] 2 tests from SimpleHistogramModuleTest (12 ms total)
35:
35: [----------] 3 tests from WeightedHistogramModuleTest
35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (7 ms)
35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (6 ms)
35: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
35: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (7 ms)
35: [----------] 3 tests from WeightedHistogramModuleTest (20 ms total)
35:
35: [----------] 3 tests from BinAverageModuleTest
35: [ RUN ] BinAverageModuleTest.ComputesCorrectly
35: [ OK ] BinAverageModuleTest.ComputesCorrectly (6 ms)
35: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
35: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (5 ms)
35: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
35: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (5 ms)
35: [----------] 3 tests from BinAverageModuleTest (16 ms total)
35:
35: [----------] 4 tests from AbstractAverageHistogramTest
35: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
35: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (11 ms)
35: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
35: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (7 ms)
35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (6 ms)
35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (7 ms)
35: [----------] 4 tests from AbstractAverageHistogramTest (31 ms total)
35:
35: [----------] 3 tests from LifetimeModuleTest
35: [ RUN ] LifetimeModuleTest.BasicTest
35: [ OK ] LifetimeModuleTest.BasicTest (4 ms)
35: [ RUN ] LifetimeModuleTest.CumulativeTest
35: [ OK ] LifetimeModuleTest.CumulativeTest (4 ms)
35: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
35: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (5 ms)
35: [----------] 3 tests from LifetimeModuleTest (13 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 69 tests from 14 test cases ran. (262 ms total)
35: [ PASSED ] 69 tests.
35/54 Test #35: AnalysisDataUnitTests ............... Passed 0.29 sec
test 36
Start 36: CoordinateIOTests
36: Test command: /<<PKGBUILDDIR>>/build/basic/bin/coordinateio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CoordinateIOTests.xml"
36: Test timeout computed to be: 30
36: [==========] Running 64 tests from 19 test cases.
36: [----------] Global test environment set-up.
36: [----------] 1 test from OutputSelectorDeathTest
36: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (12 ms)
36: [----------] 1 test from OutputSelectorDeathTest (12 ms total)
36:
36: [----------] 5 tests from TrajectoryFrameWriterTest
36: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (9 ms)
36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (9 ms)
36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (9 ms)
36: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (17 ms)
36: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks
36: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms)
36: [----------] 5 tests from TrajectoryFrameWriterTest (44 ms total)
36:
36: [----------] 5 tests from OutputAdapterContainer
36: [ RUN ] OutputAdapterContainer.MakeEmpty
36: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms)
36: [ RUN ] OutputAdapterContainer.AddAdapter
36: [ OK ] OutputAdapterContainer.AddAdapter (0 ms)
36: [ RUN ] OutputAdapterContainer.RejectBadAdapter
36: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms)
36: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter
36: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms)
36: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters
36: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms)
36: [----------] 5 tests from OutputAdapterContainer (0 ms total)
36:
36: [----------] 5 tests from FlagTest
36: [ RUN ] FlagTest.CanSetSimpleFlag
36: [ OK ] FlagTest.CanSetSimpleFlag (1 ms)
36: [ RUN ] FlagTest.CanAddNewBox
36: [ OK ] FlagTest.CanAddNewBox (0 ms)
36: [ RUN ] FlagTest.SetsImplicitPrecisionChange
36: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms)
36: [ RUN ] FlagTest.SetsImplicitStartTimeChange
36: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms)
36: [ RUN ] FlagTest.SetsImplicitTimeStepChange
36: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms)
36: [----------] 5 tests from FlagTest (1 ms total)
36:
36: [----------] 5 tests from SetAtomsTest
36: [ RUN ] SetAtomsTest.RemovesExistingAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.RemovesExistingAtoms (9 ms)
36: [ RUN ] SetAtomsTest.AddsNewAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.AddsNewAtoms (8 ms)
36: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (8 ms)
36: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (9 ms)
36: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (9 ms)
36: [----------] 5 tests from SetAtomsTest (44 ms total)
36:
36: [----------] 2 tests from SetBothTimeTest
36: [ RUN ] SetBothTimeTest.StartTimeZeroWorks
36: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms)
36: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks
36: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms)
36: [----------] 2 tests from SetBothTimeTest (0 ms total)
36:
36: [----------] 2 tests from SetStartTimeTest
36: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart
36: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms)
36: [ RUN ] SetStartTimeTest.WorksWithZeroStart
36: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms)
36: [----------] 2 tests from SetStartTimeTest (0 ms total)
36:
36: [----------] 1 test from SetTimeStepTest
36: [ RUN ] SetTimeStepTest.SetTimeStepWorks
36: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms)
36: [----------] 1 test from SetTimeStepTest (0 ms total)
36:
36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (9 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (9 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (8 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (9 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (9 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (9 ms)
36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (53 ms total)
36:
36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles
36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (8 ms)
36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (9 ms)
36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (9 ms)
36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (26 ms total)
36:
36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms)
36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total)
36:
36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (18 ms)
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (18 ms)
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (18 ms)
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (17 ms)
36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (73 ms total)
36:
36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles
36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (8 ms)
36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (9 ms)
36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (9 ms)
36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (26 ms total)
36:
36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms)
36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (0 ms total)
36:
36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles
36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (9 ms)
36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (8 ms)
36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (17 ms total)
36:
36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (1 ms)
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms)
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms)
36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (1 ms total)
36:
36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles
36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (9 ms)
36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (8 ms)
36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (17 ms total)
36:
36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (1 ms)
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms)
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms)
36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (1 ms total)
36:
36: [----------] 4 tests from ModuleSupported/NoOptionalOutput
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (9 ms)
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (8 ms)
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (9 ms)
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (9 ms)
36: [----------] 4 tests from ModuleSupported/NoOptionalOutput (35 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 64 tests from 19 test cases ran. (350 ms total)
36: [ PASSED ] 64 tests.
36/54 Test #36: CoordinateIOTests ................... Passed 0.37 sec
test 37
Start 37: TrajectoryAnalysisUnitTests
37: Test command: /<<PKGBUILDDIR>>/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
37: Test timeout computed to be: 30
37: [==========] Running 80 tests from 16 test cases.
37: [----------] Global test environment set-up.
37: [----------] 5 tests from ClustsizeTest
37: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
37: There is one group in the index
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 24
37: cmid: 2, cmax: 4, max_size: 6
37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (5 ms)
37: [ RUN ] ClustsizeTest.NoMolShortCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
37: There is one group in the index
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 24
37: cmid: 1, cmax: 6, max_size: 6
37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (5 ms)
37: [ RUN ] ClustsizeTest.MolDefaultCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 8
37: cmid: 2, cmax: 4, max_size: 2
37: 50%100%cmid: 2, cmax: 6, max_size: 2
37: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (12 ms)
37: [ RUN ] ClustsizeTest.MolShortCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 8
37: cmid: 1, cmax: 6, max_size: 2
37: 50%100%cmid: 2, cmax: 6, max_size: 2
37: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (13 ms)
37: [ RUN ] ClustsizeTest.MolCSize
37: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 8
37: cmid: 2, cmax: 4, max_size: 2
37: 50%100%cmid: 2, cmax: 6, max_size: 2
37: 50%100%[ OK ] ClustsizeTest.MolCSize (12 ms)
37: [----------] 5 tests from ClustsizeTest (47 ms total)
37:
37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (2 ms)
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
37: Reading frames from gro file 'Test system', 8 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (8 ms)
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
37: Reading frames from gro file 'Test system', 8 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (7 ms)
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (1 ms)
37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (18 ms total)
37:
37: [----------] 11 tests from AngleModuleTest
37: [ RUN ] AngleModuleTest.ComputesSimpleAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesSimpleAngles (10 ms)
37: [ RUN ] AngleModuleTest.ComputesDihedrals
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesDihedrals (10 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorPairAngles (12 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (12 ms)
37: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (10 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (11 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
37: Reading frames from gro file 'Test system for different angles', 33 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (12 ms)
37: [ RUN ] AngleModuleTest.ComputesMultipleAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesMultipleAngles (15 ms)
37: [ RUN ] AngleModuleTest.HandlesDynamicSelections
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.HandlesDynamicSelections (11 ms)
37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (11 ms)
37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (13 ms)
37: [----------] 11 tests from AngleModuleTest (128 ms total)
37:
37: [----------] 4 tests from ConvertTrjModuleTest
37: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (102 ms)
37: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (104 ms)
37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (10 ms)
37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (11 ms)
37: [----------] 4 tests from ConvertTrjModuleTest (227 ms total)
37:
37: [----------] 3 tests from DistanceModuleTest
37: [ RUN ] DistanceModuleTest.ComputesDistances
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: atomname S1 S2:
37: Number of samples: 5
37: Average distance: 1.43246 nm
37: Standard deviation: 0.96700 nm
37: [ OK ] DistanceModuleTest.ComputesDistances (13 ms)
37: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: atomname S1 S2:
37: Number of samples: 5
37: Average distance: 1.43246 nm
37: Standard deviation: 0.96700 nm
37: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
37: Number of samples: 4
37: Average distance: 1.81066 nm
37: Standard deviation: 0.79289 nm
37: [ OK ] DistanceModuleTest.ComputesMultipleDistances (18 ms)
37: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: atomname S1 S2 and res_cog x < 2.8:
37: Number of samples: 3
37: Average distance: 1.72076 nm
37: Standard deviation: 1.24839 nm
37: [ OK ] DistanceModuleTest.HandlesDynamicSelections (15 ms)
37: [----------] 3 tests from DistanceModuleTest (46 ms total)
37:
37: [----------] 2 tests from ExtractClusterModuleTest
37: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms
37: trr version: GMX_trn_file (single precision)
37:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
37: Analyzed 26 frames, last time 0.050
37: There are 8 clusters containing 26 structures, highest framenr is 25
37: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (12 ms)
37: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset
37:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
37: Analyzed 26 frames, last time 0.050
37: There are 8 clusters containing 26 structures, highest framenr is 25
37: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (12 ms)
37: [----------] 2 tests from ExtractClusterModuleTest (24 ms total)
37:
37: [----------] 2 tests from FreeVolumeModuleTest
37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for 40 particles. These were set to zero.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: cutoff = 0.18 nm
37: probe_radius = 0 nm
37: seed = 13
37: ninsert = 1000 probes per nm^3
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
37: van der Spoel and Luciano T. Costa
37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
37: -------- -------- --- Thank You --- -------- --------
37:
37: Free volume 38.02 +/- 0.00 %
37: Total volume 68.92 +/- 0.00 nm^3
37: Number of molecules 340 total mass 63491.38 Dalton
37: Average molar mass: 186.74 Dalton
37: Density rho: 1529.71 +/- 0.00 nm^3
37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
37: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
37: Fractional free volume 0.194 +/- 0.000
37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (750 ms)
37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: cutoff = 0.18 nm
37: probe_radius = 0 nm
37: seed = 17
37: ninsert = 1000 probes per nm^3
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
37: van der Spoel and Luciano T. Costa
37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
37: -------- -------- --- Thank You --- -------- --------
37:
37: Free volume 38.48 +/- 0.00 %
37: Total volume 68.92 +/- 0.00 nm^3
37: Number of molecules 340 total mass 63491.38 Dalton
37: Average molar mass: 186.74 Dalton
37: Density rho: 1529.71 +/- 0.00 nm^3
37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
37: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
37: Fractional free volume 0.200 +/- 0.000
37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (749 ms)
37: [----------] 2 tests from FreeVolumeModuleTest (1499 ms total)
37:
37: [----------] 7 tests from PairDistanceModuleTest
37: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesAllDistances (9 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (9 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (9 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (9 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (9 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (9 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (9 ms)
37: [----------] 7 tests from PairDistanceModuleTest (64 ms total)
37:
37: [----------] 5 tests from RdfModuleTest
37: [ RUN ] RdfModuleTest.BasicTest
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.BasicTest (63 ms)
37: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
37: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (42 ms)
37: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (62 ms)
37: [ RUN ] RdfModuleTest.CalculatesSurf
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.CalculatesSurf (44 ms)
37: [ RUN ] RdfModuleTest.CalculatesXY
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.CalculatesXY (70 ms)
37: [----------] 5 tests from RdfModuleTest (281 ms total)
37:
37: [----------] 5 tests from SasaModuleTest
37: [ RUN ] SasaModuleTest.BasicTest
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.BasicTest (33 ms)
37: [ RUN ] SasaModuleTest.HandlesSelectedResidues
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.HandlesSelectedResidues (21 ms)
37: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (18 ms)
37: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (27 ms)
37: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (27 ms)
37: [----------] 5 tests from SasaModuleTest (128 ms total)
37:
37: [----------] 8 tests from SelectModuleTest
37: [ RUN ] SelectModuleTest.BasicTest
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.BasicTest (18 ms)
37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (13 ms)
37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (12 ms)
37: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (13 ms)
37: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (14 ms)
37: [ RUN ] SelectModuleTest.NormalizesSizes
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.NormalizesSizes (11 ms)
37: [ RUN ] SelectModuleTest.WritesResidueNumbers
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.WritesResidueNumbers (8 ms)
37: [ RUN ] SelectModuleTest.WritesResidueIndices
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.WritesResidueIndices (8 ms)
37: [----------] 8 tests from SelectModuleTest (98 ms total)
37:
37: [----------] 10 tests from SurfaceAreaTest
37: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
37: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms)
37: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
37: [ OK ] SurfaceAreaTest.ComputesTwoPoints (3 ms)
37: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
37: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (2 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints12
37: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints32
37: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints42
37: [ OK ] SurfaceAreaTest.SurfacePoints42 (1 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints122
37: [ OK ] SurfaceAreaTest.SurfacePoints122 (2 ms)
37: [ RUN ] SurfaceAreaTest.Computes100Points
37: [ OK ] SurfaceAreaTest.Computes100Points (2 ms)
37: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
37: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (8 ms)
37: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
37: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (11 ms)
37: [----------] 10 tests from SurfaceAreaTest (30 ms total)
37:
37: [----------] 4 tests from TopologyInformation
37: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
37: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms)
37: [ RUN ] TopologyInformation.WorksWithGroFile
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TopologyInformation.WorksWithGroFile (9 ms)
37: [ RUN ] TopologyInformation.WorksWithPdbFile
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TopologyInformation.WorksWithPdbFile (8 ms)
37: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 603763677
37: Generated 330891 of the 330891 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 330891 of the 330891 1-4 parameter combinations
37: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
37:
37: NOTE 2 [file lysozyme.top, line 1465]:
37: System has non-zero total charge: 2.000000
37: Total charge should normally be an integer. See
37: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
37: for discussion on how close it should be to an integer.
37:
37:
37:
37: Number of degrees of freedom in T-Coupling group rest is 465.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
37: Analysing residue names:
37: There are: 10 Protein residues
37: Analysing Protein...
37: This run will generate roughly 0 Mb of data
37: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (971 ms)
37: [----------] 4 tests from TopologyInformation (988 ms total)
37:
37: [----------] 4 tests from TrajectoryModuleTest
37: [ RUN ] TrajectoryModuleTest.BasicTest
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.BasicTest (11 ms)
37: [ RUN ] TrajectoryModuleTest.PlotsXOnly
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.PlotsXOnly (10 ms)
37: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (9 ms)
37: [ RUN ] TrajectoryModuleTest.HandlesNoForces
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.HandlesNoForces (10 ms)
37: [----------] 4 tests from TrajectoryModuleTest (40 ms total)
37:
37: [----------] 5 tests from UnionFinderTest
37: [ RUN ] UnionFinderTest.WorksEmpty
37: [ OK ] UnionFinderTest.WorksEmpty (0 ms)
37: [ RUN ] UnionFinderTest.BasicMerges
37: [ OK ] UnionFinderTest.BasicMerges (0 ms)
37: [ RUN ] UnionFinderTest.LargerMerges
37: [ OK ] UnionFinderTest.LargerMerges (1 ms)
37: [ RUN ] UnionFinderTest.LongRightMerge
37: [ OK ] UnionFinderTest.LongRightMerge (0 ms)
37: [ RUN ] UnionFinderTest.LongLeftMerge
37: [ OK ] UnionFinderTest.LongLeftMerge (0 ms)
37: [----------] 5 tests from UnionFinderTest (1 ms total)
37:
37: [----------] 1 test from MappedUnionFinderTest
37: [ RUN ] MappedUnionFinderTest.BasicMerges
37: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms)
37: [----------] 1 test from MappedUnionFinderTest (0 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 80 tests from 16 test cases ran. (3621 ms total)
37: [ PASSED ] 80 tests.
37/54 Test #37: TrajectoryAnalysisUnitTests ......... Passed 3.65 sec
test 38
Start 38: EnergyAnalysisUnitTests
38: Test command: /<<PKGBUILDDIR>>/build/basic/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml"
38: Test timeout computed to be: 30
38: [==========] Running 7 tests from 4 test cases.
38: [----------] Global test environment set-up.
38: [----------] 1 test from DhdlTest
38: [ RUN ] DhdlTest.ExtractDhdl
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
38: Note: file tpx version 110, software tpx version 119
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
38:
38:
38: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
38: [ OK ] DhdlTest.ExtractDhdl (114 ms)
38: [----------] 1 test from DhdlTest (115 ms total)
38:
38: [----------] 1 test from OriresTest
38: [ RUN ] OriresTest.ExtractOrires
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
38: Note: file tpx version 111, software tpx version 119
38: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
38: End your selection with 0
38: Selecting all 7 orientation restraints
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
38: [ OK ] OriresTest.ExtractOrires (245 ms)
38: [----------] 1 test from OriresTest (245 ms total)
38:
38: [----------] 3 tests from EnergyTest
38: [ RUN ] EnergyTest.ExtractEnergy
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
38: Select the terms you want from the following list by
38: selecting either (part of) the name or the number or a combination.
38: End your selection with an empty line or a zero.
38: -------------------------------------------------------------------
38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
38: 13 Box-Z 14 Volume 15 Density 16 pV
38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
38:
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
38: [ OK ] EnergyTest.ExtractEnergy (26 ms)
38: [ RUN ] EnergyTest.ExtractEnergyByNumber
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
38: Select the terms you want from the following list by
38: selecting either (part of) the name or the number or a combination.
38: End your selection with an empty line or a zero.
38: -------------------------------------------------------------------
38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
38: 13 Box-Z 14 Volume 15 Density 16 pV
38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
38:
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
38: Pres. DC -268.49 3 8.52175 13.2804 (bar)
38: [ OK ] EnergyTest.ExtractEnergyByNumber (27 ms)
38: [ RUN ] EnergyTest.ExtractEnergyMixed
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
38: Select the terms you want from the following list by
38: selecting either (part of) the name or the number or a combination.
38: End your selection with an empty line or a zero.
38: -------------------------------------------------------------------
38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
38: 13 Box-Z 14 Volume 15 Density 16 pV
38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
38:
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
38: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
38: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
38: [ OK ] EnergyTest.ExtractEnergyMixed (27 ms)
38: [----------] 3 tests from EnergyTest (80 ms total)
38:
38: [----------] 2 tests from ViscosityTest
38: [ RUN ] ViscosityTest.EinsteinViscosity
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Pres-XX 20.2092 65 717.193 185.978 (bar)
38: Pres-XY -47.7351 39 372.522 207.456 (bar)
38: Pres-XZ 11.477 31 379.79 6.80818 (bar)
38: Pres-YX -47.7106 39 372.525 207.5 (bar)
38: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
38: Pres-YZ -41.3534 45 401.216 114.663 (bar)
38: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
38: Pres-ZY -41.3119 45 401.196 114.743 (bar)
38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
38: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
38: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
38: [ OK ] ViscosityTest.EinsteinViscosity (51 ms)
38: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Pres-XX 20.2092 65 717.193 185.978 (bar)
38: Pres-XY -47.7351 39 372.522 207.456 (bar)
38: Pres-XZ 11.477 31 379.79 6.80818 (bar)
38: Pres-YX -47.7106 39 372.525 207.5 (bar)
38: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
38: Pres-YZ -41.3534 45 401.216 114.663 (bar)
38: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
38: Pres-ZY -41.3119 45 401.196 114.743 (bar)
38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
38: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
38: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
38: [ OK ] ViscosityTest.EinsteinViscosityIntegral (46 ms)
38: [----------] 2 tests from ViscosityTest (98 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 7 tests from 4 test cases ran. (539 ms total)
38: [ PASSED ] 7 tests.
38/54 Test #38: EnergyAnalysisUnitTests ............. Passed 0.56 sec
test 39
Start 39: ToolUnitTests
39: Test command: /<<PKGBUILDDIR>>/build/basic/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/ToolUnitTests.xml"
39: Test timeout computed to be: 30
39: [==========] Running 18 tests from 4 test cases.
39: [----------] Global test environment set-up.
39: [----------] 2 tests from DumpTest
39:
39: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
39: For a correct single-point energy evaluation with nsteps = 0, use
39: continuation = yes to avoid constraining the input coordinates.
39:
39: Setting the LD random seed to 1333927100
39: Generated 330891 of the 330891 non-bonded parameter combinations
39: Generating 1-4 interactions: fudge = 0.5
39: Generated 330891 of the 330891 1-4 parameter combinations
39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
39:
39: NOTE 2 [file lysozyme.top, line 1465]:
39: System has non-zero total charge: 2.000000
39: Total charge should normally be an integer. See
39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
39: for discussion on how close it should be to an integer.
39:
39:
39:
39: Number of degrees of freedom in T-Coupling group rest is 465.00
39:
39: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
39: NVE simulation with an initial temperature of zero: will use a Verlet
39: buffer of 10%. Check your energy drift!
39:
39:
39: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
39: You are using a plain Coulomb cut-off, which might produce artifacts.
39: You might want to consider using PME electrostatics.
39:
39:
39:
39: There were 4 notes
39: Analysing residue names:
39: There are: 10 Protein residues
39: Analysing Protein...
39: This run will generate roughly 0 Mb of data
39: [ RUN ] DumpTest.WorksWithTpr
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
39: /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr:
39: inputrec:
39: integrator = md
39: tinit = 0
39: dt = 0.001
39: nsteps = 0
39: init-step = 0
39: simulation-part = 1
39: comm-mode = Linear
39: nstcomm = 100
39: bd-fric = 0
39: ld-seed = 1333927100
39: emtol = 10
39: emstep = 0.01
39: niter = 20
39: fcstep = 0
39: nstcgsteep = 1000
39: nbfgscorr = 10
39: rtpi = 0.05
39: nstxout = 0
39: nstvout = 0
39: nstfout = 0
39: nstlog = 1000
39: nstcalcenergy = 100
39: nstenergy = 1000
39: nstxout-compressed = 0
39: compressed-x-precision = 1000
39: cutoff-scheme = Verlet
39: nstlist = 10
39: pbc = xyz
39: periodic-molecules = false
39: verlet-buffer-tolerance = -1
39: rlist = 1.1
39: coulombtype = Cut-off
39: coulomb-modifier = Potential-shift
39: rcoulomb-switch = 0
39: rcoulomb = 1
39: epsilon-r = 1
39: epsilon-rf = inf
39: vdw-type = Cut-off
39: vdw-modifier = Potential-shift
39: rvdw-switch = 0
39: rvdw = 1
39: DispCorr = No
39: table-extension = 1
39: fourierspacing = 0.12
39: fourier-nx = 0
39: fourier-ny = 0
39: fourier-nz = 0
39: pme-order = 4
39: ewald-rtol = 1e-05
39: ewald-rtol-lj = 0.001
39: lj-pme-comb-rule = Geometric
39: ewald-geometry = 0
39: epsilon-surface = 0
39: tcoupl = No
39: nsttcouple = -1
39: nh-chain-length = 0
39: print-nose-hoover-chain-variables = false
39: pcoupl = No
39: pcoupltype = Isotropic
39: nstpcouple = -1
39: tau-p = 1
39: compressibility (3x3):
39: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: ref-p (3x3):
39: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: refcoord-scaling = No
39: posres-com (3):
39: posres-com[0]= 0.00000e+00
39: posres-com[1]= 0.00000e+00
39: posres-com[2]= 0.00000e+00
39: posres-comB (3):
39: posres-comB[0]= 0.00000e+00
39: posres-comB[1]= 0.00000e+00
39: posres-comB[2]= 0.00000e+00
39: QMMM = false
39: QMconstraints = 0
39: QMMMscheme = 0
39: MMChargeScaleFactor = 1
39: qm-opts:
39: ngQM = 0
39: constraint-algorithm = Lincs
39: continuation = false
39: Shake-SOR = false
39: shake-tol = 0.0001
39: lincs-order = 4
39: lincs-iter = 1
39: lincs-warnangle = 30
39: nwall = 0
39: wall-type = 9-3
39: wall-r-linpot = -1
39: wall-atomtype[0] = -1
39: wall-atomtype[1] = -1
39: wall-density[0] = 0
39: wall-density[1] = 0
39: wall-ewald-zfac = 3
39: pull = false
39: awh = false
39: rotation = false
39: interactiveMD = false
39: disre = No
39: disre-weighting = Conservative
39: disre-mixed = false
39: dr-fc = 1000
39: dr-tau = 0
39: nstdisreout = 100
39: orire-fc = 0
39: orire-tau = 0
39: nstorireout = 100
39: free-energy = no
39: cos-acceleration = 0
39: deform (3x3):
39: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: simulated-tempering = false
39: swapcoords = no
39: userint1 = 0
39: userint2 = 0
39: userint3 = 0
39: userint4 = 0
39: userreal1 = 0
39: userreal2 = 0
39: userreal3 = 0
39: userreal4 = 0
39: applied-forces:
39: electric-field:
39: x:
39: E0 = 0
39: omega = 0
39: t0 = 0
39: sigma = 0
39: y:
39: E0 = 0
39: omega = 0
39: t0 = 0
39: sigma = 0
39: z:
39: E0 = 0
39: omega = 0
39: t0 = 0
39: sigma = 0
39: density-guided-simulation:
39: active = false
39: group = protein
39: similarity-measure = inner-product
39: atom-spreading-weight = unity
39: force-constant = 1e+09
39: gaussian-transform-spreading-width = 0.2
39: gaussian-transform-spreading-range-in-multiples-of-width = 4
39: reference-density-filename = reference.mrc
39: nst = 1
39: normalize-densities = true
39: adaptive-force-scaling = false
39: adaptive-force-scaling-time-constant = 4
39: grpopts:
39: nrdf: 465
39: ref-t: 0
39: tau-t: 0
39: annealing: No
39: annealing-npoints: 0
39: acc: 0 0 0
39: nfreeze: N N N
39: energygrp-flags[ 0]: 0
39: header:
39: bIr = present
39: bBox = present
39: bTop = present
39: bX = present
39: bV = present
39: bF = not present
39: natoms = 156
39: lambda = 0.000000e+00
39: buffer size = 59422
39: topology:
39: name="First 10 residues from 1AKI"
39: #atoms = 156
39: #molblock = 1
39: molblock (0):
39: moltype = 0 "Protein_chain_B"
39: #molecules = 1
39: #posres_xA = 0
39: #posres_xB = 0
39: bIntermolecularInteractions = false
39: ffparams:
39: atnr=10
39: ntypes=212
39: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06
39: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06
39: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07
39: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06
39: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06
39: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06
39: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07
39: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07
39: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05
39: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
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39: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
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39: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
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39: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06
39: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06
39: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07
39: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06
39: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06
39: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06
39: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07
39: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07
39: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05
39: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07
39: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07
39: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08
39: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07
39: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07
39: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07
39: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08
39: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08
39: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06
39: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06
39: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06
39: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07
39: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05
39: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06
39: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06
39: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07
39: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07
39: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05
39: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06
39: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06
39: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07
39: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06
39: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06
39: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06
39: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07
39: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07
39: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06
39: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06
39: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06
39: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07
39: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06
39: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06
39: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06
39: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07
39: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07
39: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05
39: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07
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39: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07
39: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08
39: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07
39: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07
39: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07
39: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08
39: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08
39: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07
39: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07
39: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07
39: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08
39: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07
39: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07
39: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07
39: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08
39: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08
39: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07
39: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05
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39: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05
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39: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05
39: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06
39: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05
39: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07
39: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07
39: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05
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39: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05
39: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05
39: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05
39: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05
39: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05
39: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05
39: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05
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39: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05
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39: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02
39: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02
39: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02
39: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02
39: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02
39: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02
39: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02
39: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02
39: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02
39: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02
39: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02
39: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02
39: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02
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39: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02
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39: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02
39: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02
39: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02
39: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02
39: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02
39: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02
39: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2
39: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2
39: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2
39: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07
39: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06
39: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06
39: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06
39: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00
39: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07
39: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06
39: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08
39: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07
39: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06
39: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07
39: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06
39: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06
39: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06
39: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06
39: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07
39: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07
39: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07
39: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06
39: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06
39: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08
39: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07
39: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08
39: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06
39: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07
39: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05
39: reppow = 12
39: fudgeQQ = 0.5
39: cmap
39: atomtypes:
39: atomtype[ 0]={atomnumber= 7}
39: atomtype[ 1]={atomnumber= 1}
39: atomtype[ 2]={atomnumber= 6}
39: atomtype[ 3]={atomnumber= 1}
39: atomtype[ 4]={atomnumber= 6}
39: atomtype[ 5]={atomnumber= 8}
39: atomtype[ 6]={atomnumber= 6}
39: atomtype[ 7]={atomnumber= 1}
39: atomtype[ 8]={atomnumber= 6}
39: atomtype[ 9]={atomnumber= 16}
39: moltype (0):
39: name="Protein_chain_B"
39: atoms:
39: atom (156):
39: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
39: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6}
39: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
39: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
39: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
39: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6}
39: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
39: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6}
39: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8}
39: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7}
39: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1}
39: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6}
39: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6}
39: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
39: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
39: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6}
39: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8}
39: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7}
39: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1}
39: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6}
39: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
39: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6}
39: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
39: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
39: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6}
39: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8}
39: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7}
39: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1}
39: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6}
39: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
39: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
39: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6}
39: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8}
39: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1}
39: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6}
39: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6}
39: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6}
39: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6}
39: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1}
39: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6}
39: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6}
39: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8}
39: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7}
39: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1}
39: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6}
39: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
39: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6}
39: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
39: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
39: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16}
39: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1}
39: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6}
39: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8}
39: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7}
39: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1}
39: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6}
39: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6}
39: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6}
39: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6}
39: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
39: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
39: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6}
39: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8}
39: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7}
39: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1}
39: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6}
39: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6}
39: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6}
39: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
39: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
39: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6}
39: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8}
39: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7}
39: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1}
39: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6}
39: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6}
39: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6}
39: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8}
39: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7}
39: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1}
39: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6}
39: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6}
39: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6}
39: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8}
39: atom (156):
39: atom[0]={name="N"}
39: atom[1]={name="H1"}
39: atom[2]={name="H2"}
39: atom[3]={name="H3"}
39: atom[4]={name="CA"}
39: atom[5]={name="HA"}
39: atom[6]={name="CB"}
39: atom[7]={name="HB1"}
39: atom[8]={name="HB2"}
39: atom[9]={name="CG"}
39: atom[10]={name="HG1"}
39: atom[11]={name="HG2"}
39: atom[12]={name="CD"}
39: atom[13]={name="HD1"}
39: atom[14]={name="HD2"}
39: atom[15]={name="CE"}
39: atom[16]={name="HE1"}
39: atom[17]={name="HE2"}
39: atom[18]={name="NZ"}
39: atom[19]={name="HZ1"}
39: atom[20]={name="HZ2"}
39: atom[21]={name="HZ3"}
39: atom[22]={name="C"}
39: atom[23]={name="O"}
39: atom[24]={name="N"}
39: atom[25]={name="H"}
39: atom[26]={name="CA"}
39: atom[27]={name="HA"}
39: atom[28]={name="CB"}
39: atom[29]={name="HB"}
39: atom[30]={name="CG1"}
39: atom[31]={name="HG11"}
39: atom[32]={name="HG12"}
39: atom[33]={name="HG13"}
39: atom[34]={name="CG2"}
39: atom[35]={name="HG21"}
39: atom[36]={name="HG22"}
39: atom[37]={name="HG23"}
39: atom[38]={name="C"}
39: atom[39]={name="O"}
39: atom[40]={name="N"}
39: atom[41]={name="H"}
39: atom[42]={name="CA"}
39: atom[43]={name="HA"}
39: atom[44]={name="CB"}
39: atom[45]={name="HB1"}
39: atom[46]={name="HB2"}
39: atom[47]={name="CG"}
39: atom[48]={name="CD1"}
39: atom[49]={name="HD1"}
39: atom[50]={name="CD2"}
39: atom[51]={name="HD2"}
39: atom[52]={name="CE1"}
39: atom[53]={name="HE1"}
39: atom[54]={name="CE2"}
39: atom[55]={name="HE2"}
39: atom[56]={name="CZ"}
39: atom[57]={name="HZ"}
39: atom[58]={name="C"}
39: atom[59]={name="O"}
39: atom[60]={name="N"}
39: atom[61]={name="H"}
39: atom[62]={name="CA"}
39: atom[63]={name="HA1"}
39: atom[64]={name="HA2"}
39: atom[65]={name="C"}
39: atom[66]={name="O"}
39: atom[67]={name="N"}
39: atom[68]={name="H"}
39: atom[69]={name="CA"}
39: atom[70]={name="HA"}
39: atom[71]={name="CB"}
39: atom[72]={name="HB1"}
39: atom[73]={name="HB2"}
39: atom[74]={name="CG"}
39: atom[75]={name="HG1"}
39: atom[76]={name="HG2"}
39: atom[77]={name="CD"}
39: atom[78]={name="HD1"}
39: atom[79]={name="HD2"}
39: atom[80]={name="NE"}
39: atom[81]={name="HE"}
39: atom[82]={name="CZ"}
39: atom[83]={name="NH1"}
39: atom[84]={name="HH11"}
39: atom[85]={name="HH12"}
39: atom[86]={name="NH2"}
39: atom[87]={name="HH21"}
39: atom[88]={name="HH22"}
39: atom[89]={name="C"}
39: atom[90]={name="O"}
39: atom[91]={name="N"}
39: atom[92]={name="H"}
39: atom[93]={name="CA"}
39: atom[94]={name="HA"}
39: atom[95]={name="CB"}
39: atom[96]={name="HB1"}
39: atom[97]={name="HB2"}
39: atom[98]={name="SG"}
39: atom[99]={name="HG"}
39: atom[100]={name="C"}
39: atom[101]={name="O"}
39: atom[102]={name="N"}
39: atom[103]={name="H"}
39: atom[104]={name="CA"}
39: atom[105]={name="HA"}
39: atom[106]={name="CB"}
39: atom[107]={name="HB1"}
39: atom[108]={name="HB2"}
39: atom[109]={name="CG"}
39: atom[110]={name="HG1"}
39: atom[111]={name="HG2"}
39: atom[112]={name="CD"}
39: atom[113]={name="OE1"}
39: atom[114]={name="OE2"}
39: atom[115]={name="C"}
39: atom[116]={name="O"}
39: atom[117]={name="N"}
39: atom[118]={name="H"}
39: atom[119]={name="CA"}
39: atom[120]={name="HA"}
39: atom[121]={name="CB"}
39: atom[122]={name="HB1"}
39: atom[123]={name="HB2"}
39: atom[124]={name="CG"}
39: atom[125]={name="HG"}
39: atom[126]={name="CD1"}
39: atom[127]={name="HD11"}
39: atom[128]={name="HD12"}
39: atom[129]={name="HD13"}
39: atom[130]={name="CD2"}
39: atom[131]={name="HD21"}
39: atom[132]={name="HD22"}
39: atom[133]={name="HD23"}
39: atom[134]={name="C"}
39: atom[135]={name="O"}
39: atom[136]={name="N"}
39: atom[137]={name="H"}
39: atom[138]={name="CA"}
39: atom[139]={name="HA"}
39: atom[140]={name="CB"}
39: atom[141]={name="HB1"}
39: atom[142]={name="HB2"}
39: atom[143]={name="HB3"}
39: atom[144]={name="C"}
39: atom[145]={name="O"}
39: atom[146]={name="N"}
39: atom[147]={name="H"}
39: atom[148]={name="CA"}
39: atom[149]={name="HA"}
39: atom[150]={name="CB"}
39: atom[151]={name="HB1"}
39: atom[152]={name="HB2"}
39: atom[153]={name="HB3"}
39: atom[154]={name="C"}
39: atom[155]={name="O"}
39: type (156):
39: type[0]={name="opls_287",nameB="opls_287"}
39: type[1]={name="opls_290",nameB="opls_290"}
39: type[2]={name="opls_290",nameB="opls_290"}
39: type[3]={name="opls_290",nameB="opls_290"}
39: type[4]={name="opls_293B",nameB="opls_293B"}
39: type[5]={name="opls_140",nameB="opls_140"}
39: type[6]={name="opls_136",nameB="opls_136"}
39: type[7]={name="opls_140",nameB="opls_140"}
39: type[8]={name="opls_140",nameB="opls_140"}
39: type[9]={name="opls_136",nameB="opls_136"}
39: type[10]={name="opls_140",nameB="opls_140"}
39: type[11]={name="opls_140",nameB="opls_140"}
39: type[12]={name="opls_136",nameB="opls_136"}
39: type[13]={name="opls_140",nameB="opls_140"}
39: type[14]={name="opls_140",nameB="opls_140"}
39: type[15]={name="opls_292",nameB="opls_292"}
39: type[16]={name="opls_140",nameB="opls_140"}
39: type[17]={name="opls_140",nameB="opls_140"}
39: type[18]={name="opls_287",nameB="opls_287"}
39: type[19]={name="opls_290",nameB="opls_290"}
39: type[20]={name="opls_290",nameB="opls_290"}
39: type[21]={name="opls_290",nameB="opls_290"}
39: type[22]={name="opls_235",nameB="opls_235"}
39: type[23]={name="opls_236",nameB="opls_236"}
39: type[24]={name="opls_238",nameB="opls_238"}
39: type[25]={name="opls_241",nameB="opls_241"}
39: type[26]={name="opls_224B",nameB="opls_224B"}
39: type[27]={name="opls_140",nameB="opls_140"}
39: type[28]={name="opls_137",nameB="opls_137"}
39: type[29]={name="opls_140",nameB="opls_140"}
39: type[30]={name="opls_135",nameB="opls_135"}
39: type[31]={name="opls_140",nameB="opls_140"}
39: type[32]={name="opls_140",nameB="opls_140"}
39: type[33]={name="opls_140",nameB="opls_140"}
39: type[34]={name="opls_135",nameB="opls_135"}
39: type[35]={name="opls_140",nameB="opls_140"}
39: type[36]={name="opls_140",nameB="opls_140"}
39: type[37]={name="opls_140",nameB="opls_140"}
39: type[38]={name="opls_235",nameB="opls_235"}
39: type[39]={name="opls_236",nameB="opls_236"}
39: type[40]={name="opls_238",nameB="opls_238"}
39: type[41]={name="opls_241",nameB="opls_241"}
39: type[42]={name="opls_224B",nameB="opls_224B"}
39: type[43]={name="opls_140",nameB="opls_140"}
39: type[44]={name="opls_149",nameB="opls_149"}
39: type[45]={name="opls_140",nameB="opls_140"}
39: type[46]={name="opls_140",nameB="opls_140"}
39: type[47]={name="opls_145",nameB="opls_145"}
39: type[48]={name="opls_145",nameB="opls_145"}
39: type[49]={name="opls_146",nameB="opls_146"}
39: type[50]={name="opls_145",nameB="opls_145"}
39: type[51]={name="opls_146",nameB="opls_146"}
39: type[52]={name="opls_145",nameB="opls_145"}
39: type[53]={name="opls_146",nameB="opls_146"}
39: type[54]={name="opls_145",nameB="opls_145"}
39: type[55]={name="opls_146",nameB="opls_146"}
39: type[56]={name="opls_145",nameB="opls_145"}
39: type[57]={name="opls_146",nameB="opls_146"}
39: type[58]={name="opls_235",nameB="opls_235"}
39: type[59]={name="opls_236",nameB="opls_236"}
39: type[60]={name="opls_238",nameB="opls_238"}
39: type[61]={name="opls_241",nameB="opls_241"}
39: type[62]={name="opls_223B",nameB="opls_223B"}
39: type[63]={name="opls_140",nameB="opls_140"}
39: type[64]={name="opls_140",nameB="opls_140"}
39: type[65]={name="opls_235",nameB="opls_235"}
39: type[66]={name="opls_236",nameB="opls_236"}
39: type[67]={name="opls_238",nameB="opls_238"}
39: type[68]={name="opls_241",nameB="opls_241"}
39: type[69]={name="opls_224B",nameB="opls_224B"}
39: type[70]={name="opls_140",nameB="opls_140"}
39: type[71]={name="opls_136",nameB="opls_136"}
39: type[72]={name="opls_140",nameB="opls_140"}
39: type[73]={name="opls_140",nameB="opls_140"}
39: type[74]={name="opls_308",nameB="opls_308"}
39: type[75]={name="opls_140",nameB="opls_140"}
39: type[76]={name="opls_140",nameB="opls_140"}
39: type[77]={name="opls_307",nameB="opls_307"}
39: type[78]={name="opls_140",nameB="opls_140"}
39: type[79]={name="opls_140",nameB="opls_140"}
39: type[80]={name="opls_303",nameB="opls_303"}
39: type[81]={name="opls_304",nameB="opls_304"}
39: type[82]={name="opls_302",nameB="opls_302"}
39: type[83]={name="opls_300",nameB="opls_300"}
39: type[84]={name="opls_301",nameB="opls_301"}
39: type[85]={name="opls_301",nameB="opls_301"}
39: type[86]={name="opls_300",nameB="opls_300"}
39: type[87]={name="opls_301",nameB="opls_301"}
39: type[88]={name="opls_301",nameB="opls_301"}
39: type[89]={name="opls_235",nameB="opls_235"}
39: type[90]={name="opls_236",nameB="opls_236"}
39: type[91]={name="opls_238",nameB="opls_238"}
39: type[92]={name="opls_241",nameB="opls_241"}
39: type[93]={name="opls_224B",nameB="opls_224B"}
39: type[94]={name="opls_140",nameB="opls_140"}
39: type[95]={name="opls_206",nameB="opls_206"}
39: type[96]={name="opls_140",nameB="opls_140"}
39: type[97]={name="opls_140",nameB="opls_140"}
39: type[98]={name="opls_200",nameB="opls_200"}
39: type[99]={name="opls_204",nameB="opls_204"}
39: type[100]={name="opls_235",nameB="opls_235"}
39: type[101]={name="opls_236",nameB="opls_236"}
39: type[102]={name="opls_238",nameB="opls_238"}
39: type[103]={name="opls_241",nameB="opls_241"}
39: type[104]={name="opls_224B",nameB="opls_224B"}
39: type[105]={name="opls_140",nameB="opls_140"}
39: type[106]={name="opls_136",nameB="opls_136"}
39: type[107]={name="opls_140",nameB="opls_140"}
39: type[108]={name="opls_140",nameB="opls_140"}
39: type[109]={name="opls_274",nameB="opls_274"}
39: type[110]={name="opls_140",nameB="opls_140"}
39: type[111]={name="opls_140",nameB="opls_140"}
39: type[112]={name="opls_271",nameB="opls_271"}
39: type[113]={name="opls_272",nameB="opls_272"}
39: type[114]={name="opls_272",nameB="opls_272"}
39: type[115]={name="opls_235",nameB="opls_235"}
39: type[116]={name="opls_236",nameB="opls_236"}
39: type[117]={name="opls_238",nameB="opls_238"}
39: type[118]={name="opls_241",nameB="opls_241"}
39: type[119]={name="opls_224B",nameB="opls_224B"}
39: type[120]={name="opls_140",nameB="opls_140"}
39: type[121]={name="opls_136",nameB="opls_136"}
39: type[122]={name="opls_140",nameB="opls_140"}
39: type[123]={name="opls_140",nameB="opls_140"}
39: type[124]={name="opls_137",nameB="opls_137"}
39: type[125]={name="opls_140",nameB="opls_140"}
39: type[126]={name="opls_135",nameB="opls_135"}
39: type[127]={name="opls_140",nameB="opls_140"}
39: type[128]={name="opls_140",nameB="opls_140"}
39: type[129]={name="opls_140",nameB="opls_140"}
39: type[130]={name="opls_135",nameB="opls_135"}
39: type[131]={name="opls_140",nameB="opls_140"}
39: type[132]={name="opls_140",nameB="opls_140"}
39: type[133]={name="opls_140",nameB="opls_140"}
39: type[134]={name="opls_235",nameB="opls_235"}
39: type[135]={name="opls_236",nameB="opls_236"}
39: type[136]={name="opls_238",nameB="opls_238"}
39: type[137]={name="opls_241",nameB="opls_241"}
39: type[138]={name="opls_224B",nameB="opls_224B"}
39: type[139]={name="opls_140",nameB="opls_140"}
39: type[140]={name="opls_135",nameB="opls_135"}
39: type[141]={name="opls_140",nameB="opls_140"}
39: type[142]={name="opls_140",nameB="opls_140"}
39: type[143]={name="opls_140",nameB="opls_140"}
39: type[144]={name="opls_235",nameB="opls_235"}
39: type[145]={name="opls_236",nameB="opls_236"}
39: type[146]={name="opls_238",nameB="opls_238"}
39: type[147]={name="opls_241",nameB="opls_241"}
39: type[148]={name="opls_224B",nameB="opls_224B"}
39: type[149]={name="opls_140",nameB="opls_140"}
39: type[150]={name="opls_135",nameB="opls_135"}
39: type[151]={name="opls_140",nameB="opls_140"}
39: type[152]={name="opls_140",nameB="opls_140"}
39: type[153]={name="opls_140",nameB="opls_140"}
39: type[154]={name="opls_235",nameB="opls_235"}
39: type[155]={name="opls_236",nameB="opls_236"}
39: residue (10):
39: residue[0]={name="LYS", nr=1, ic=' '}
39: residue[1]={name="VAL", nr=2, ic=' '}
39: residue[2]={name="PHE", nr=3, ic=' '}
39: residue[3]={name="GLY", nr=4, ic=' '}
39: residue[4]={name="ARG", nr=5, ic=' '}
39: residue[5]={name="CYS", nr=6, ic=' '}
39: residue[6]={name="GLU", nr=7, ic=' '}
39: residue[7]={name="LEU", nr=8, ic=' '}
39: residue[8]={name="ALA", nr=9, ic=' '}
39: residue[9]={name="ALA", nr=10, ic=' '}
39: excls:
39: nr=156
39: nra=1828
39: excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
39: excls[1][13..20]={0, 1, 2, 3, 4, 5, 6, 22}
39: excls[2][21..28]={0, 1, 2, 3, 4, 5, 6, 22}
39: excls[3][29..36]={0, 1, 2, 3, 4, 5, 6, 22}
39: excls[4][37..54]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22,
39: 23, 24, 25, 26}
39: excls[5][55..67]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
39: excls[6][68..86]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
39: 14, 15, 22, 23, 24}
39: excls[7][87..97]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
39: excls[8][98..108]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
39: excls[9][109..125]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
39: 16, 17, 18, 22}
39: excls[10][126..136]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
39: excls[11][137..147]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
39: excls[12][148..164]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
39: 17, 18, 19, 20, 21}
39: excls[13][165..175]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
39: excls[14][176..186]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
39: excls[15][187..200]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
39: 19, 20, 21}
39: excls[16][201..211]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
39: excls[17][212..222]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
39: excls[18][223..233]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
39: excls[19][234..241]={12, 15, 16, 17, 18, 19, 20, 21}
39: excls[20][242..249]={12, 15, 16, 17, 18, 19, 20, 21}
39: excls[21][250..257]={12, 15, 16, 17, 18, 19, 20, 21}
39: excls[22][258..275]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24,
39: 25, 26, 27, 28, 38}
39: excls[23][276..284]={0, 4, 5, 6, 22, 23, 24, 25, 26}
39: excls[24][285..301]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29,
39: 30, 34, 38, 39, 40}
39: excls[25][302..310]={4, 22, 23, 24, 25, 26, 27, 28, 38}
39: excls[26][311..332]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
39: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42}
39: excls[27][333..344]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
39: 40}
39: excls[28][345..362]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
39: 34, 35, 36, 37, 38, 39, 40}
39: excls[29][363..376]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
39: 36, 37, 38}
39: excls[30][377..390]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
39: 36, 37, 38}
39: excls[31][391..398]={26, 28, 29, 30, 31, 32, 33, 34}
39: excls[32][399..406]={26, 28, 29, 30, 31, 32, 33, 34}
39: excls[33][407..414]={26, 28, 29, 30, 31, 32, 33, 34}
39: excls[34][415..428]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
39: 36, 37, 38}
39: excls[35][429..436]={26, 28, 29, 30, 34, 35, 36, 37}
39: excls[36][437..444]={26, 28, 29, 30, 34, 35, 36, 37}
39: excls[37][445..452]={26, 28, 29, 30, 34, 35, 36, 37}
39: excls[38][453..469]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
39: 40, 41, 42, 43, 44, 58}
39: excls[39][470..478]={24, 26, 27, 28, 38, 39, 40, 41, 42}
39: excls[40][479..495]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44,
39: 45, 46, 47, 58, 59, 60}
39: excls[41][496..504]={26, 38, 39, 40, 41, 42, 43, 44, 58}
39: excls[42][505..522]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
39: 48, 50, 58, 59, 60, 61, 62}
39: excls[43][523..534]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
39: 60}
39: excls[44][535..552]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
39: 50, 51, 52, 54, 58, 59, 60}
39: excls[45][553..562]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
39: excls[46][563..572]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
39: excls[47][573..589]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
39: 52, 53, 54, 55, 56, 58}
39: excls[48][590..603]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
39: 54, 56, 57}
39: excls[49][604..611]={44, 47, 48, 49, 50, 52, 53, 56}
39: excls[50][612..625]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54,
39: 55, 56, 57}
39: excls[51][626..633]={44, 47, 48, 50, 51, 54, 55, 56}
39: excls[52][634..644]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57}
39: excls[53][645..652]={47, 48, 49, 52, 53, 54, 56, 57}
39: excls[54][653..663]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57}
39: excls[55][664..671]={47, 50, 51, 52, 54, 55, 56, 57}
39: excls[56][672..682]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57}
39: excls[57][683..690]={48, 50, 52, 53, 54, 55, 56, 57}
39: excls[58][691..707]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
39: 60, 61, 62, 63, 64, 65}
39: excls[59][708..716]={40, 42, 43, 44, 58, 59, 60, 61, 62}
39: excls[60][717..730]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64,
39: 65, 66, 67}
39: excls[61][731..739]={42, 58, 59, 60, 61, 62, 63, 64, 65}
39: excls[62][740..752]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
39: 68, 69}
39: excls[63][753..761]={58, 60, 61, 62, 63, 64, 65, 66, 67}
39: excls[64][762..770]={58, 60, 61, 62, 63, 64, 65, 66, 67}
39: excls[65][771..784]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
39: 70, 71, 89}
39: excls[66][785..793]={60, 62, 63, 64, 65, 66, 67, 68, 69}
39: excls[67][794..810]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
39: 72, 73, 74, 89, 90, 91}
39: excls[68][811..819]={62, 65, 66, 67, 68, 69, 70, 71, 89}
39: excls[69][820..838]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
39: 75, 76, 77, 89, 90, 91, 92, 93}
39: excls[70][839..850]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
39: 91}
39: excls[71][851..868]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
39: 77, 78, 79, 80, 89, 90, 91}
39: excls[72][869..879]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
39: excls[73][880..890]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
39: excls[74][891..906]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
39: 79, 80, 81, 82, 89}
39: excls[75][907..917]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
39: excls[76][918..928]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
39: excls[77][929..943]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
39: 81, 82, 83, 86}
39: excls[78][944..953]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
39: excls[79][954..963]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
39: excls[80][964..979]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,
39: 84, 85, 86, 87, 88}
39: excls[81][980..988]={74, 77, 78, 79, 80, 81, 82, 83, 86}
39: excls[82][989..1001]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85,
39: 86, 87, 88}
39: excls[83][1002..1011]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
39: excls[84][1012..1017]={80, 82, 83, 84, 85, 86}
39: excls[85][1018..1023]={80, 82, 83, 84, 85, 86}
39: excls[86][1024..1033]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
39: excls[87][1034..1039]={80, 82, 83, 86, 87, 88}
39: excls[88][1040..1045]={80, 82, 83, 86, 87, 88}
39: excls[89][1046..1062]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89,
39: 90, 91, 92, 93, 94, 95, 100}
39: excls[90][1063..1071]={67, 69, 70, 71, 89, 90, 91, 92, 93}
39: excls[91][1072..1088]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94,
39: 95, 96, 97, 98, 100, 101, 102}
39: excls[92][1089..1097]={69, 89, 90, 91, 92, 93, 94, 95, 100}
39: excls[93][1098..1114]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97,
39: 98, 99, 100, 101, 102, 103, 104}
39: excls[94][1115..1126]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
39: 101, 102}
39: excls[95][1127..1139]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99,
39: 100, 101, 102}
39: excls[96][1140..1148]={91, 93, 94, 95, 96, 97, 98, 99, 100}
39: excls[97][1149..1157]={91, 93, 94, 95, 96, 97, 98, 99, 100}
39: excls[98][1158..1166]={91, 93, 94, 95, 96, 97, 98, 99, 100}
39: excls[99][1167..1172]={93, 95, 96, 97, 98, 99}
39: excls[100][1173..1189]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
39: 101, 102, 103, 104, 105, 106, 115}
39: excls[101][1190..1198]={91, 93, 94, 95, 100, 101, 102, 103, 104}
39: excls[102][1199..1215]={91, 93, 94, 95, 100, 101, 102, 103, 104,
39: 105, 106, 107, 108, 109, 115, 116, 117}
39: excls[103][1216..1224]={93, 100, 101, 102, 103, 104, 105, 106,
39: 115}
39: excls[104][1225..1243]={93, 100, 101, 102, 103, 104, 105, 106,
39: 107, 108, 109, 110, 111, 112, 115, 116, 117, 118, 119}
39: excls[105][1244..1255]={100, 102, 103, 104, 105, 106, 107, 108,
39: 109, 115, 116, 117}
39: excls[106][1256..1272]={100, 102, 103, 104, 105, 106, 107, 108,
39: 109, 110, 111, 112, 113, 114, 115, 116, 117}
39: excls[107][1273..1283]={102, 104, 105, 106, 107, 108, 109, 110,
39: 111, 112, 115}
39: excls[108][1284..1294]={102, 104, 105, 106, 107, 108, 109, 110,
39: 111, 112, 115}
39: excls[109][1295..1307]={102, 104, 105, 106, 107, 108, 109, 110,
39: 111, 112, 113, 114, 115}
39: excls[110][1308..1317]={104, 106, 107, 108, 109, 110, 111, 112,
39: 113, 114}
39: excls[111][1318..1327]={104, 106, 107, 108, 109, 110, 111, 112,
39: 113, 114}
39: excls[112][1328..1337]={104, 106, 107, 108, 109, 110, 111, 112,
39: 113, 114}
39: excls[113][1338..1344]={106, 109, 110, 111, 112, 113, 114}
39: excls[114][1345..1351]={106, 109, 110, 111, 112, 113, 114}
39: excls[115][1352..1368]={100, 102, 103, 104, 105, 106, 107, 108,
39: 109, 115, 116, 117, 118, 119, 120, 121, 134}
39: excls[116][1369..1377]={102, 104, 105, 106, 115, 116, 117, 118,
39: 119}
39: excls[117][1378..1394]={102, 104, 105, 106, 115, 116, 117, 118,
39: 119, 120, 121, 122, 123, 124, 134, 135, 136}
39: excls[118][1395..1403]={104, 115, 116, 117, 118, 119, 120, 121,
39: 134}
39: excls[119][1404..1422]={104, 115, 116, 117, 118, 119, 120, 121,
39: 122, 123, 124, 125, 126, 130, 134, 135, 136, 137, 138}
39: excls[120][1423..1434]={115, 117, 118, 119, 120, 121, 122, 123,
39: 124, 134, 135, 136}
39: excls[121][1435..1455]={115, 117, 118, 119, 120, 121, 122, 123,
39: 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135,
39: 136}
39: excls[122][1456..1466]={117, 119, 120, 121, 122, 123, 124, 125,
39: 126, 130, 134}
39: excls[123][1467..1477]={117, 119, 120, 121, 122, 123, 124, 125,
39: 126, 130, 134}
39: excls[124][1478..1494]={117, 119, 120, 121, 122, 123, 124, 125,
39: 126, 127, 128, 129, 130, 131, 132, 133, 134}
39: excls[125][1495..1508]={119, 121, 122, 123, 124, 125, 126, 127,
39: 128, 129, 130, 131, 132, 133}
39: excls[126][1509..1522]={119, 121, 122, 123, 124, 125, 126, 127,
39: 128, 129, 130, 131, 132, 133}
39: excls[127][1523..1530]={121, 124, 125, 126, 127, 128, 129, 130}
39: excls[128][1531..1538]={121, 124, 125, 126, 127, 128, 129, 130}
39: excls[129][1539..1546]={121, 124, 125, 126, 127, 128, 129, 130}
39: excls[130][1547..1560]={119, 121, 122, 123, 124, 125, 126, 127,
39: 128, 129, 130, 131, 132, 133}
39: excls[131][1561..1568]={121, 124, 125, 126, 130, 131, 132, 133}
39: excls[132][1569..1576]={121, 124, 125, 126, 130, 131, 132, 133}
39: excls[133][1577..1584]={121, 124, 125, 126, 130, 131, 132, 133}
39: excls[134][1585..1601]={115, 117, 118, 119, 120, 121, 122, 123,
39: 124, 134, 135, 136, 137, 138, 139, 140, 144}
39: excls[135][1602..1610]={117, 119, 120, 121, 134, 135, 136, 137,
39: 138}
39: excls[136][1611..1627]={117, 119, 120, 121, 134, 135, 136, 137,
39: 138, 139, 140, 141, 142, 143, 144, 145, 146}
39: excls[137][1628..1636]={119, 134, 135, 136, 137, 138, 139, 140,
39: 144}
39: excls[138][1637..1652]={119, 134, 135, 136, 137, 138, 139, 140,
39: 141, 142, 143, 144, 145, 146, 147, 148}
39: excls[139][1653..1664]={134, 136, 137, 138, 139, 140, 141, 142,
39: 143, 144, 145, 146}
39: excls[140][1665..1676]={134, 136, 137, 138, 139, 140, 141, 142,
39: 143, 144, 145, 146}
39: excls[141][1677..1684]={136, 138, 139, 140, 141, 142, 143, 144}
39: excls[142][1685..1692]={136, 138, 139, 140, 141, 142, 143, 144}
39: excls[143][1693..1700]={136, 138, 139, 140, 141, 142, 143, 144}
39: excls[144][1701..1717]={134, 136, 137, 138, 139, 140, 141, 142,
39: 143, 144, 145, 146, 147, 148, 149, 150, 154}
39: excls[145][1718..1726]={136, 138, 139, 140, 144, 145, 146, 147,
39: 148}
39: excls[146][1727..1742]={136, 138, 139, 140, 144, 145, 146, 147,
39: 148, 149, 150, 151, 152, 153, 154, 155}
39: excls[147][1743..1751]={138, 144, 145, 146, 147, 148, 149, 150,
39: 154}
39: excls[148][1752..1764]={138, 144, 145, 146, 147, 148, 149, 150,
39: 151, 152, 153, 154, 155}
39: excls[149][1765..1775]={144, 146, 147, 148, 149, 150, 151, 152,
39: 153, 154, 155}
39: excls[150][1776..1786]={144, 146, 147, 148, 149, 150, 151, 152,
39: 153, 154, 155}
39: excls[151][1787..1794]={146, 148, 149, 150, 151, 152, 153, 154}
39: excls[152][1795..1802]={146, 148, 149, 150, 151, 152, 153, 154}
39: excls[153][1803..1810]={146, 148, 149, 150, 151, 152, 153, 154}
39: excls[154][1811..1821]={144, 146, 147, 148, 149, 150, 151, 152,
39: 153, 154, 155}
39: excls[155][1822..1827]={146, 148, 149, 150, 154, 155}
39: Bond:
39: nr: 468
39: iatoms:
39: 0 type=100 (BONDS) 0 1
39: 1 type=100 (BONDS) 0 2
39: 2 type=100 (BONDS) 0 3
39: 3 type=101 (BONDS) 0 4
39: 4 type=102 (BONDS) 4 5
39: 5 type=103 (BONDS) 4 6
39: 6 type=104 (BONDS) 4 22
39: 7 type=102 (BONDS) 6 7
39: 8 type=102 (BONDS) 6 8
39: 9 type=103 (BONDS) 6 9
39: 10 type=102 (BONDS) 9 10
39: 11 type=102 (BONDS) 9 11
39: 12 type=103 (BONDS) 9 12
39: 13 type=102 (BONDS) 12 13
39: 14 type=102 (BONDS) 12 14
39: 15 type=103 (BONDS) 12 15
39: 16 type=102 (BONDS) 15 16
39: 17 type=102 (BONDS) 15 17
39: 18 type=101 (BONDS) 15 18
39: 19 type=100 (BONDS) 18 19
39: 20 type=100 (BONDS) 18 20
39: 21 type=100 (BONDS) 18 21
39: 22 type=105 (BONDS) 22 23
39: 23 type=106 (BONDS) 22 24
39: 24 type=100 (BONDS) 24 25
39: 25 type=107 (BONDS) 24 26
39: 26 type=102 (BONDS) 26 27
39: 27 type=103 (BONDS) 26 28
39: 28 type=104 (BONDS) 26 38
39: 29 type=102 (BONDS) 28 29
39: 30 type=103 (BONDS) 28 30
39: 31 type=103 (BONDS) 28 34
39: 32 type=102 (BONDS) 30 31
39: 33 type=102 (BONDS) 30 32
39: 34 type=102 (BONDS) 30 33
39: 35 type=102 (BONDS) 34 35
39: 36 type=102 (BONDS) 34 36
39: 37 type=102 (BONDS) 34 37
39: 38 type=105 (BONDS) 38 39
39: 39 type=106 (BONDS) 38 40
39: 40 type=100 (BONDS) 40 41
39: 41 type=107 (BONDS) 40 42
39: 42 type=102 (BONDS) 42 43
39: 43 type=103 (BONDS) 42 44
39: 44 type=104 (BONDS) 42 58
39: 45 type=102 (BONDS) 44 45
39: 46 type=102 (BONDS) 44 46
39: 47 type=108 (BONDS) 44 47
39: 48 type=109 (BONDS) 47 48
39: 49 type=109 (BONDS) 47 50
39: 50 type=110 (BONDS) 48 49
39: 51 type=109 (BONDS) 48 52
39: 52 type=110 (BONDS) 50 51
39: 53 type=109 (BONDS) 50 54
39: 54 type=110 (BONDS) 52 53
39: 55 type=109 (BONDS) 52 56
39: 56 type=110 (BONDS) 54 55
39: 57 type=109 (BONDS) 54 56
39: 58 type=110 (BONDS) 56 57
39: 59 type=105 (BONDS) 58 59
39: 60 type=106 (BONDS) 58 60
39: 61 type=100 (BONDS) 60 61
39: 62 type=107 (BONDS) 60 62
39: 63 type=102 (BONDS) 62 63
39: 64 type=102 (BONDS) 62 64
39: 65 type=104 (BONDS) 62 65
39: 66 type=105 (BONDS) 65 66
39: 67 type=106 (BONDS) 65 67
39: 68 type=100 (BONDS) 67 68
39: 69 type=107 (BONDS) 67 69
39: 70 type=102 (BONDS) 69 70
39: 71 type=103 (BONDS) 69 71
39: 72 type=104 (BONDS) 69 89
39: 73 type=102 (BONDS) 71 72
39: 74 type=102 (BONDS) 71 73
39: 75 type=103 (BONDS) 71 74
39: 76 type=102 (BONDS) 74 75
39: 77 type=102 (BONDS) 74 76
39: 78 type=103 (BONDS) 74 77
39: 79 type=102 (BONDS) 77 78
39: 80 type=102 (BONDS) 77 79
39: 81 type=111 (BONDS) 77 80
39: 82 type=100 (BONDS) 80 81
39: 83 type=112 (BONDS) 80 82
39: 84 type=112 (BONDS) 82 83
39: 85 type=112 (BONDS) 82 86
39: 86 type=100 (BONDS) 83 84
39: 87 type=100 (BONDS) 83 85
39: 88 type=100 (BONDS) 86 87
39: 89 type=100 (BONDS) 86 88
39: 90 type=105 (BONDS) 89 90
39: 91 type=106 (BONDS) 89 91
39: 92 type=100 (BONDS) 91 92
39: 93 type=107 (BONDS) 91 93
39: 94 type=102 (BONDS) 93 94
39: 95 type=103 (BONDS) 93 95
39: 96 type=104 (BONDS) 93 100
39: 97 type=102 (BONDS) 95 96
39: 98 type=102 (BONDS) 95 97
39: 99 type=113 (BONDS) 95 98
39: 100 type=114 (BONDS) 98 99
39: 101 type=105 (BONDS) 100 101
39: 102 type=106 (BONDS) 100 102
39: 103 type=100 (BONDS) 102 103
39: 104 type=107 (BONDS) 102 104
39: 105 type=102 (BONDS) 104 105
39: 106 type=103 (BONDS) 104 106
39: 107 type=104 (BONDS) 104 115
39: 108 type=102 (BONDS) 106 107
39: 109 type=102 (BONDS) 106 108
39: 110 type=103 (BONDS) 106 109
39: 111 type=102 (BONDS) 109 110
39: 112 type=102 (BONDS) 109 111
39: 113 type=104 (BONDS) 109 112
39: 114 type=115 (BONDS) 112 113
39: 115 type=115 (BONDS) 112 114
39: 116 type=105 (BONDS) 115 116
39: 117 type=106 (BONDS) 115 117
39: 118 type=100 (BONDS) 117 118
39: 119 type=107 (BONDS) 117 119
39: 120 type=102 (BONDS) 119 120
39: 121 type=103 (BONDS) 119 121
39: 122 type=104 (BONDS) 119 134
39: 123 type=102 (BONDS) 121 122
39: 124 type=102 (BONDS) 121 123
39: 125 type=103 (BONDS) 121 124
39: 126 type=102 (BONDS) 124 125
39: 127 type=103 (BONDS) 124 126
39: 128 type=103 (BONDS) 124 130
39: 129 type=102 (BONDS) 126 127
39: 130 type=102 (BONDS) 126 128
39: 131 type=102 (BONDS) 126 129
39: 132 type=102 (BONDS) 130 131
39: 133 type=102 (BONDS) 130 132
39: 134 type=102 (BONDS) 130 133
39: 135 type=105 (BONDS) 134 135
39: 136 type=106 (BONDS) 134 136
39: 137 type=100 (BONDS) 136 137
39: 138 type=107 (BONDS) 136 138
39: 139 type=102 (BONDS) 138 139
39: 140 type=103 (BONDS) 138 140
39: 141 type=104 (BONDS) 138 144
39: 142 type=102 (BONDS) 140 141
39: 143 type=102 (BONDS) 140 142
39: 144 type=102 (BONDS) 140 143
39: 145 type=105 (BONDS) 144 145
39: 146 type=106 (BONDS) 144 146
39: 147 type=100 (BONDS) 146 147
39: 148 type=107 (BONDS) 146 148
39: 149 type=102 (BONDS) 148 149
39: 150 type=103 (BONDS) 148 150
39: 151 type=104 (BONDS) 148 154
39: 152 type=102 (BONDS) 150 151
39: 153 type=102 (BONDS) 150 152
39: 154 type=102 (BONDS) 150 153
39: 155 type=105 (BONDS) 154 155
39: G96Bond:
39: nr: 0
39: Morse:
39: nr: 0
39: Cubic Bonds:
39: nr: 0
39: Connect Bonds:
39: nr: 0
39: Harmonic Pot.:
39: nr: 0
39: FENE Bonds:
39: nr: 0
39: Tab. Bonds:
39: nr: 0
39: Tab. Bonds NC:
39: nr: 0
39: Restraint Pot.:
39: nr: 0
39: Angle:
39: nr: 1124
39: iatoms:
39: 0 type=116 (ANGLES) 1 0 2
39: 1 type=116 (ANGLES) 1 0 3
39: 2 type=116 (ANGLES) 1 0 4
39: 3 type=116 (ANGLES) 2 0 3
39: 4 type=116 (ANGLES) 2 0 4
39: 5 type=116 (ANGLES) 3 0 4
39: 6 type=116 (ANGLES) 0 4 5
39: 7 type=117 (ANGLES) 0 4 6
39: 8 type=117 (ANGLES) 0 4 22
39: 9 type=118 (ANGLES) 5 4 6
39: 10 type=116 (ANGLES) 5 4 22
39: 11 type=119 (ANGLES) 6 4 22
39: 12 type=118 (ANGLES) 4 6 7
39: 13 type=118 (ANGLES) 4 6 8
39: 14 type=120 (ANGLES) 4 6 9
39: 15 type=121 (ANGLES) 7 6 8
39: 16 type=118 (ANGLES) 7 6 9
39: 17 type=118 (ANGLES) 8 6 9
39: 18 type=118 (ANGLES) 6 9 10
39: 19 type=118 (ANGLES) 6 9 11
39: 20 type=120 (ANGLES) 6 9 12
39: 21 type=121 (ANGLES) 10 9 11
39: 22 type=118 (ANGLES) 10 9 12
39: 23 type=118 (ANGLES) 11 9 12
39: 24 type=118 (ANGLES) 9 12 13
39: 25 type=118 (ANGLES) 9 12 14
39: 26 type=120 (ANGLES) 9 12 15
39: 27 type=121 (ANGLES) 13 12 14
39: 28 type=118 (ANGLES) 13 12 15
39: 29 type=118 (ANGLES) 14 12 15
39: 30 type=118 (ANGLES) 12 15 16
39: 31 type=118 (ANGLES) 12 15 17
39: 32 type=117 (ANGLES) 12 15 18
39: 33 type=121 (ANGLES) 16 15 17
39: 34 type=116 (ANGLES) 16 15 18
39: 35 type=116 (ANGLES) 17 15 18
39: 36 type=116 (ANGLES) 15 18 19
39: 37 type=116 (ANGLES) 15 18 20
39: 38 type=116 (ANGLES) 15 18 21
39: 39 type=116 (ANGLES) 19 18 20
39: 40 type=116 (ANGLES) 19 18 21
39: 41 type=116 (ANGLES) 20 18 21
39: 42 type=122 (ANGLES) 4 22 23
39: 43 type=123 (ANGLES) 4 22 24
39: 44 type=124 (ANGLES) 23 22 24
39: 45 type=125 (ANGLES) 22 24 25
39: 46 type=126 (ANGLES) 22 24 26
39: 47 type=127 (ANGLES) 25 24 26
39: 48 type=116 (ANGLES) 24 26 27
39: 49 type=128 (ANGLES) 24 26 28
39: 50 type=129 (ANGLES) 24 26 38
39: 51 type=118 (ANGLES) 27 26 28
39: 52 type=116 (ANGLES) 27 26 38
39: 53 type=119 (ANGLES) 28 26 38
39: 54 type=118 (ANGLES) 26 28 29
39: 55 type=120 (ANGLES) 26 28 30
39: 56 type=120 (ANGLES) 26 28 34
39: 57 type=118 (ANGLES) 29 28 30
39: 58 type=118 (ANGLES) 29 28 34
39: 59 type=120 (ANGLES) 30 28 34
39: 60 type=118 (ANGLES) 28 30 31
39: 61 type=118 (ANGLES) 28 30 32
39: 62 type=118 (ANGLES) 28 30 33
39: 63 type=121 (ANGLES) 31 30 32
39: 64 type=121 (ANGLES) 31 30 33
39: 65 type=121 (ANGLES) 32 30 33
39: 66 type=118 (ANGLES) 28 34 35
39: 67 type=118 (ANGLES) 28 34 36
39: 68 type=118 (ANGLES) 28 34 37
39: 69 type=121 (ANGLES) 35 34 36
39: 70 type=121 (ANGLES) 35 34 37
39: 71 type=121 (ANGLES) 36 34 37
39: 72 type=122 (ANGLES) 26 38 39
39: 73 type=123 (ANGLES) 26 38 40
39: 74 type=124 (ANGLES) 39 38 40
39: 75 type=125 (ANGLES) 38 40 41
39: 76 type=126 (ANGLES) 38 40 42
39: 77 type=127 (ANGLES) 41 40 42
39: 78 type=116 (ANGLES) 40 42 43
39: 79 type=128 (ANGLES) 40 42 44
39: 80 type=129 (ANGLES) 40 42 58
39: 81 type=118 (ANGLES) 43 42 44
39: 82 type=116 (ANGLES) 43 42 58
39: 83 type=119 (ANGLES) 44 42 58
39: 84 type=118 (ANGLES) 42 44 45
39: 85 type=118 (ANGLES) 42 44 46
39: 86 type=130 (ANGLES) 42 44 47
39: 87 type=121 (ANGLES) 45 44 46
39: 88 type=116 (ANGLES) 45 44 47
39: 89 type=116 (ANGLES) 46 44 47
39: 90 type=131 (ANGLES) 44 47 48
39: 91 type=131 (ANGLES) 44 47 50
39: 92 type=132 (ANGLES) 48 47 50
39: 93 type=133 (ANGLES) 47 48 49
39: 94 type=132 (ANGLES) 47 48 52
39: 95 type=133 (ANGLES) 49 48 52
39: 96 type=133 (ANGLES) 47 50 51
39: 97 type=132 (ANGLES) 47 50 54
39: 98 type=133 (ANGLES) 51 50 54
39: 99 type=133 (ANGLES) 48 52 53
39: 100 type=132 (ANGLES) 48 52 56
39: 101 type=133 (ANGLES) 53 52 56
39: 102 type=133 (ANGLES) 50 54 55
39: 103 type=132 (ANGLES) 50 54 56
39: 104 type=133 (ANGLES) 55 54 56
39: 105 type=132 (ANGLES) 52 56 54
39: 106 type=133 (ANGLES) 52 56 57
39: 107 type=133 (ANGLES) 54 56 57
39: 108 type=122 (ANGLES) 42 58 59
39: 109 type=123 (ANGLES) 42 58 60
39: 110 type=124 (ANGLES) 59 58 60
39: 111 type=125 (ANGLES) 58 60 61
39: 112 type=126 (ANGLES) 58 60 62
39: 113 type=127 (ANGLES) 61 60 62
39: 114 type=116 (ANGLES) 60 62 63
39: 115 type=116 (ANGLES) 60 62 64
39: 116 type=129 (ANGLES) 60 62 65
39: 117 type=121 (ANGLES) 63 62 64
39: 118 type=116 (ANGLES) 63 62 65
39: 119 type=116 (ANGLES) 64 62 65
39: 120 type=122 (ANGLES) 62 65 66
39: 121 type=123 (ANGLES) 62 65 67
39: 122 type=124 (ANGLES) 66 65 67
39: 123 type=125 (ANGLES) 65 67 68
39: 124 type=126 (ANGLES) 65 67 69
39: 125 type=127 (ANGLES) 68 67 69
39: 126 type=116 (ANGLES) 67 69 70
39: 127 type=128 (ANGLES) 67 69 71
39: 128 type=129 (ANGLES) 67 69 89
39: 129 type=118 (ANGLES) 70 69 71
39: 130 type=116 (ANGLES) 70 69 89
39: 131 type=119 (ANGLES) 71 69 89
39: 132 type=118 (ANGLES) 69 71 72
39: 133 type=118 (ANGLES) 69 71 73
39: 134 type=120 (ANGLES) 69 71 74
39: 135 type=121 (ANGLES) 72 71 73
39: 136 type=118 (ANGLES) 72 71 74
39: 137 type=118 (ANGLES) 73 71 74
39: 138 type=118 (ANGLES) 71 74 75
39: 139 type=118 (ANGLES) 71 74 76
39: 140 type=120 (ANGLES) 71 74 77
39: 141 type=121 (ANGLES) 75 74 76
39: 142 type=118 (ANGLES) 75 74 77
39: 143 type=118 (ANGLES) 76 74 77
39: 144 type=118 (ANGLES) 74 77 78
39: 145 type=118 (ANGLES) 74 77 79
39: 146 type=117 (ANGLES) 74 77 80
39: 147 type=121 (ANGLES) 78 77 79
39: 148 type=116 (ANGLES) 78 77 80
39: 149 type=116 (ANGLES) 79 77 80
39: 150 type=134 (ANGLES) 77 80 81
39: 151 type=135 (ANGLES) 77 80 82
39: 152 type=133 (ANGLES) 81 80 82
39: 153 type=131 (ANGLES) 80 82 83
39: 154 type=131 (ANGLES) 80 82 86
39: 155 type=131 (ANGLES) 83 82 86
39: 156 type=133 (ANGLES) 82 83 84
39: 157 type=133 (ANGLES) 82 83 85
39: 158 type=133 (ANGLES) 84 83 85
39: 159 type=133 (ANGLES) 82 86 87
39: 160 type=133 (ANGLES) 82 86 88
39: 161 type=133 (ANGLES) 87 86 88
39: 162 type=122 (ANGLES) 69 89 90
39: 163 type=123 (ANGLES) 69 89 91
39: 164 type=124 (ANGLES) 90 89 91
39: 165 type=125 (ANGLES) 89 91 92
39: 166 type=126 (ANGLES) 89 91 93
39: 167 type=127 (ANGLES) 92 91 93
39: 168 type=116 (ANGLES) 91 93 94
39: 169 type=128 (ANGLES) 91 93 95
39: 170 type=129 (ANGLES) 91 93 100
39: 171 type=118 (ANGLES) 94 93 95
39: 172 type=116 (ANGLES) 94 93 100
39: 173 type=119 (ANGLES) 95 93 100
39: 174 type=118 (ANGLES) 93 95 96
39: 175 type=118 (ANGLES) 93 95 97
39: 176 type=136 (ANGLES) 93 95 98
39: 177 type=121 (ANGLES) 96 95 97
39: 178 type=116 (ANGLES) 96 95 98
39: 179 type=116 (ANGLES) 97 95 98
39: 180 type=137 (ANGLES) 95 98 99
39: 181 type=122 (ANGLES) 93 100 101
39: 182 type=123 (ANGLES) 93 100 102
39: 183 type=124 (ANGLES) 101 100 102
39: 184 type=125 (ANGLES) 100 102 103
39: 185 type=126 (ANGLES) 100 102 104
39: 186 type=127 (ANGLES) 103 102 104
39: 187 type=116 (ANGLES) 102 104 105
39: 188 type=128 (ANGLES) 102 104 106
39: 189 type=129 (ANGLES) 102 104 115
39: 190 type=118 (ANGLES) 105 104 106
39: 191 type=116 (ANGLES) 105 104 115
39: 192 type=119 (ANGLES) 106 104 115
39: 193 type=118 (ANGLES) 104 106 107
39: 194 type=118 (ANGLES) 104 106 108
39: 195 type=120 (ANGLES) 104 106 109
39: 196 type=121 (ANGLES) 107 106 108
39: 197 type=118 (ANGLES) 107 106 109
39: 198 type=118 (ANGLES) 108 106 109
39: 199 type=118 (ANGLES) 106 109 110
39: 200 type=118 (ANGLES) 106 109 111
39: 201 type=119 (ANGLES) 106 109 112
39: 202 type=121 (ANGLES) 110 109 111
39: 203 type=116 (ANGLES) 110 109 112
39: 204 type=116 (ANGLES) 111 109 112
39: 205 type=138 (ANGLES) 109 112 113
39: 206 type=138 (ANGLES) 109 112 114
39: 207 type=139 (ANGLES) 113 112 114
39: 208 type=122 (ANGLES) 104 115 116
39: 209 type=123 (ANGLES) 104 115 117
39: 210 type=124 (ANGLES) 116 115 117
39: 211 type=125 (ANGLES) 115 117 118
39: 212 type=126 (ANGLES) 115 117 119
39: 213 type=127 (ANGLES) 118 117 119
39: 214 type=116 (ANGLES) 117 119 120
39: 215 type=128 (ANGLES) 117 119 121
39: 216 type=129 (ANGLES) 117 119 134
39: 217 type=118 (ANGLES) 120 119 121
39: 218 type=116 (ANGLES) 120 119 134
39: 219 type=119 (ANGLES) 121 119 134
39: 220 type=118 (ANGLES) 119 121 122
39: 221 type=118 (ANGLES) 119 121 123
39: 222 type=120 (ANGLES) 119 121 124
39: 223 type=121 (ANGLES) 122 121 123
39: 224 type=118 (ANGLES) 122 121 124
39: 225 type=118 (ANGLES) 123 121 124
39: 226 type=118 (ANGLES) 121 124 125
39: 227 type=120 (ANGLES) 121 124 126
39: 228 type=120 (ANGLES) 121 124 130
39: 229 type=118 (ANGLES) 125 124 126
39: 230 type=118 (ANGLES) 125 124 130
39: 231 type=120 (ANGLES) 126 124 130
39: 232 type=118 (ANGLES) 124 126 127
39: 233 type=118 (ANGLES) 124 126 128
39: 234 type=118 (ANGLES) 124 126 129
39: 235 type=121 (ANGLES) 127 126 128
39: 236 type=121 (ANGLES) 127 126 129
39: 237 type=121 (ANGLES) 128 126 129
39: 238 type=118 (ANGLES) 124 130 131
39: 239 type=118 (ANGLES) 124 130 132
39: 240 type=118 (ANGLES) 124 130 133
39: 241 type=121 (ANGLES) 131 130 132
39: 242 type=121 (ANGLES) 131 130 133
39: 243 type=121 (ANGLES) 132 130 133
39: 244 type=122 (ANGLES) 119 134 135
39: 245 type=123 (ANGLES) 119 134 136
39: 246 type=124 (ANGLES) 135 134 136
39: 247 type=125 (ANGLES) 134 136 137
39: 248 type=126 (ANGLES) 134 136 138
39: 249 type=127 (ANGLES) 137 136 138
39: 250 type=116 (ANGLES) 136 138 139
39: 251 type=128 (ANGLES) 136 138 140
39: 252 type=129 (ANGLES) 136 138 144
39: 253 type=118 (ANGLES) 139 138 140
39: 254 type=116 (ANGLES) 139 138 144
39: 255 type=119 (ANGLES) 140 138 144
39: 256 type=118 (ANGLES) 138 140 141
39: 257 type=118 (ANGLES) 138 140 142
39: 258 type=118 (ANGLES) 138 140 143
39: 259 type=121 (ANGLES) 141 140 142
39: 260 type=121 (ANGLES) 141 140 143
39: 261 type=121 (ANGLES) 142 140 143
39: 262 type=122 (ANGLES) 138 144 145
39: 263 type=123 (ANGLES) 138 144 146
39: 264 type=124 (ANGLES) 145 144 146
39: 265 type=125 (ANGLES) 144 146 147
39: 266 type=126 (ANGLES) 144 146 148
39: 267 type=127 (ANGLES) 147 146 148
39: 268 type=116 (ANGLES) 146 148 149
39: 269 type=128 (ANGLES) 146 148 150
39: 270 type=129 (ANGLES) 146 148 154
39: 271 type=118 (ANGLES) 149 148 150
39: 272 type=116 (ANGLES) 149 148 154
39: 273 type=119 (ANGLES) 150 148 154
39: 274 type=118 (ANGLES) 148 150 151
39: 275 type=118 (ANGLES) 148 150 152
39: 276 type=118 (ANGLES) 148 150 153
39: 277 type=121 (ANGLES) 151 150 152
39: 278 type=121 (ANGLES) 151 150 153
39: 279 type=121 (ANGLES) 152 150 153
39: 280 type=122 (ANGLES) 148 154 155
39: G96Angle:
39: nr: 0
39: Restricted Angles:
39: nr: 0
39: Lin. Angle:
39: nr: 0
39: Bond-Cross:
39: nr: 0
39: BA-Cross:
39: nr: 0
39: U-B:
39: nr: 0
39: Quartic Angles:
39: nr: 0
39: Tab. Angles:
39: nr: 0
39: Proper Dih.:
39: nr: 145
39: iatoms:
39: 0 type=140 (PDIHS) 4 24 22 23
39: 1 type=141 (PDIHS) 22 26 24 25
39: 2 type=140 (PDIHS) 26 40 38 39
39: 3 type=141 (PDIHS) 38 42 40 41
39: 4 type=140 (PDIHS) 42 60 58 59
39: 5 type=142 (PDIHS) 44 47 50 48
39: 6 type=142 (PDIHS) 47 52 48 49
39: 7 type=142 (PDIHS) 47 54 50 51
39: 8 type=142 (PDIHS) 48 56 52 53
39: 9 type=142 (PDIHS) 50 56 54 55
39: 10 type=142 (PDIHS) 52 54 56 57
39: 11 type=141 (PDIHS) 58 62 60 61
39: 12 type=140 (PDIHS) 62 67 65 66
39: 13 type=141 (PDIHS) 65 69 67 68
39: 14 type=140 (PDIHS) 69 91 89 90
39: 15 type=141 (PDIHS) 77 82 80 81
39: 16 type=140 (PDIHS) 80 83 82 86
39: 17 type=141 (PDIHS) 82 84 83 85
39: 18 type=141 (PDIHS) 82 87 86 88
39: 19 type=141 (PDIHS) 89 93 91 92
39: 20 type=140 (PDIHS) 93 102 100 101
39: 21 type=141 (PDIHS) 100 104 102 103
39: 22 type=140 (PDIHS) 104 117 115 116
39: 23 type=140 (PDIHS) 109 113 112 114
39: 24 type=141 (PDIHS) 115 119 117 118
39: 25 type=140 (PDIHS) 119 136 134 135
39: 26 type=141 (PDIHS) 134 138 136 137
39: 27 type=140 (PDIHS) 138 146 144 145
39: 28 type=141 (PDIHS) 144 148 146 147
39: Ryckaert-Bell.:
39: nr: 1565
39: iatoms:
39: 0 type=143 (RBDIHS) 1 0 4 5
39: 1 type=144 (RBDIHS) 1 0 4 6
39: 2 type=144 (RBDIHS) 1 0 4 22
39: 3 type=143 (RBDIHS) 2 0 4 5
39: 4 type=144 (RBDIHS) 2 0 4 6
39: 5 type=144 (RBDIHS) 2 0 4 22
39: 6 type=143 (RBDIHS) 3 0 4 5
39: 7 type=144 (RBDIHS) 3 0 4 6
39: 8 type=144 (RBDIHS) 3 0 4 22
39: 9 type=145 (RBDIHS) 0 4 6 9
39: 10 type=146 (RBDIHS) 22 4 6 9
39: 11 type=147 (RBDIHS) 0 4 6 7
39: 12 type=147 (RBDIHS) 0 4 6 8
39: 13 type=148 (RBDIHS) 5 4 6 7
39: 14 type=148 (RBDIHS) 5 4 6 8
39: 15 type=148 (RBDIHS) 5 4 6 9
39: 16 type=149 (RBDIHS) 22 4 6 7
39: 17 type=149 (RBDIHS) 22 4 6 8
39: 18 type=150 (RBDIHS) 0 4 22 24
39: 19 type=151 (RBDIHS) 6 4 22 24
39: 20 type=148 (RBDIHS) 4 6 9 10
39: 21 type=148 (RBDIHS) 4 6 9 11
39: 22 type=152 (RBDIHS) 4 6 9 12
39: 23 type=148 (RBDIHS) 7 6 9 10
39: 24 type=148 (RBDIHS) 7 6 9 11
39: 25 type=148 (RBDIHS) 7 6 9 12
39: 26 type=148 (RBDIHS) 8 6 9 10
39: 27 type=148 (RBDIHS) 8 6 9 11
39: 28 type=148 (RBDIHS) 8 6 9 12
39: 29 type=148 (RBDIHS) 6 9 12 13
39: 30 type=148 (RBDIHS) 6 9 12 14
39: 31 type=152 (RBDIHS) 6 9 12 15
39: 32 type=148 (RBDIHS) 10 9 12 13
39: 33 type=148 (RBDIHS) 10 9 12 14
39: 34 type=148 (RBDIHS) 10 9 12 15
39: 35 type=148 (RBDIHS) 11 9 12 13
39: 36 type=148 (RBDIHS) 11 9 12 14
39: 37 type=148 (RBDIHS) 11 9 12 15
39: 38 type=148 (RBDIHS) 9 12 15 16
39: 39 type=148 (RBDIHS) 9 12 15 17
39: 40 type=153 (RBDIHS) 9 12 15 18
39: 41 type=148 (RBDIHS) 13 12 15 16
39: 42 type=148 (RBDIHS) 13 12 15 17
39: 43 type=154 (RBDIHS) 13 12 15 18
39: 44 type=148 (RBDIHS) 14 12 15 16
39: 45 type=148 (RBDIHS) 14 12 15 17
39: 46 type=154 (RBDIHS) 14 12 15 18
39: 47 type=144 (RBDIHS) 12 15 18 19
39: 48 type=144 (RBDIHS) 12 15 18 20
39: 49 type=144 (RBDIHS) 12 15 18 21
39: 50 type=143 (RBDIHS) 16 15 18 19
39: 51 type=143 (RBDIHS) 16 15 18 20
39: 52 type=143 (RBDIHS) 16 15 18 21
39: 53 type=143 (RBDIHS) 17 15 18 19
39: 54 type=143 (RBDIHS) 17 15 18 20
39: 55 type=143 (RBDIHS) 17 15 18 21
39: 56 type=155 (RBDIHS) 4 22 24 25
39: 57 type=156 (RBDIHS) 4 22 24 26
39: 58 type=155 (RBDIHS) 23 22 24 25
39: 59 type=157 (RBDIHS) 23 22 24 26
39: 60 type=158 (RBDIHS) 22 24 26 28
39: 61 type=159 (RBDIHS) 22 24 26 38
39: 62 type=160 (RBDIHS) 24 26 28 30
39: 63 type=160 (RBDIHS) 24 26 28 34
39: 64 type=161 (RBDIHS) 38 26 28 30
39: 65 type=161 (RBDIHS) 38 26 28 34
39: 66 type=147 (RBDIHS) 24 26 28 29
39: 67 type=148 (RBDIHS) 27 26 28 29
39: 68 type=148 (RBDIHS) 27 26 28 30
39: 69 type=148 (RBDIHS) 27 26 28 34
39: 70 type=149 (RBDIHS) 38 26 28 29
39: 71 type=150 (RBDIHS) 24 26 38 40
39: 72 type=151 (RBDIHS) 28 26 38 40
39: 73 type=148 (RBDIHS) 26 28 30 31
39: 74 type=148 (RBDIHS) 26 28 30 32
39: 75 type=148 (RBDIHS) 26 28 30 33
39: 76 type=148 (RBDIHS) 29 28 30 31
39: 77 type=148 (RBDIHS) 29 28 30 32
39: 78 type=148 (RBDIHS) 29 28 30 33
39: 79 type=148 (RBDIHS) 34 28 30 31
39: 80 type=148 (RBDIHS) 34 28 30 32
39: 81 type=148 (RBDIHS) 34 28 30 33
39: 82 type=148 (RBDIHS) 26 28 34 35
39: 83 type=148 (RBDIHS) 26 28 34 36
39: 84 type=148 (RBDIHS) 26 28 34 37
39: 85 type=148 (RBDIHS) 29 28 34 35
39: 86 type=148 (RBDIHS) 29 28 34 36
39: 87 type=148 (RBDIHS) 29 28 34 37
39: 88 type=148 (RBDIHS) 30 28 34 35
39: 89 type=148 (RBDIHS) 30 28 34 36
39: 90 type=148 (RBDIHS) 30 28 34 37
39: 91 type=155 (RBDIHS) 26 38 40 41
39: 92 type=156 (RBDIHS) 26 38 40 42
39: 93 type=155 (RBDIHS) 39 38 40 41
39: 94 type=157 (RBDIHS) 39 38 40 42
39: 95 type=158 (RBDIHS) 38 40 42 44
39: 96 type=159 (RBDIHS) 38 40 42 58
39: 97 type=147 (RBDIHS) 40 42 44 45
39: 98 type=147 (RBDIHS) 40 42 44 46
39: 99 type=162 (RBDIHS) 40 42 44 47
39: 100 type=148 (RBDIHS) 43 42 44 45
39: 101 type=148 (RBDIHS) 43 42 44 46
39: 102 type=163 (RBDIHS) 43 42 44 47
39: 103 type=149 (RBDIHS) 58 42 44 45
39: 104 type=149 (RBDIHS) 58 42 44 46
39: 105 type=164 (RBDIHS) 58 42 44 47
39: 106 type=150 (RBDIHS) 40 42 58 60
39: 107 type=151 (RBDIHS) 44 42 58 60
39: 108 type=165 (RBDIHS) 44 47 48 49
39: 109 type=165 (RBDIHS) 44 47 48 52
39: 110 type=165 (RBDIHS) 50 47 48 49
39: 111 type=165 (RBDIHS) 50 47 48 52
39: 112 type=165 (RBDIHS) 44 47 50 51
39: 113 type=165 (RBDIHS) 44 47 50 54
39: 114 type=165 (RBDIHS) 48 47 50 51
39: 115 type=165 (RBDIHS) 48 47 50 54
39: 116 type=165 (RBDIHS) 47 48 52 53
39: 117 type=165 (RBDIHS) 47 48 52 56
39: 118 type=165 (RBDIHS) 49 48 52 53
39: 119 type=165 (RBDIHS) 49 48 52 56
39: 120 type=165 (RBDIHS) 47 50 54 55
39: 121 type=165 (RBDIHS) 47 50 54 56
39: 122 type=165 (RBDIHS) 51 50 54 55
39: 123 type=165 (RBDIHS) 51 50 54 56
39: 124 type=165 (RBDIHS) 48 52 56 54
39: 125 type=165 (RBDIHS) 48 52 56 57
39: 126 type=165 (RBDIHS) 53 52 56 54
39: 127 type=165 (RBDIHS) 53 52 56 57
39: 128 type=165 (RBDIHS) 50 54 56 52
39: 129 type=165 (RBDIHS) 50 54 56 57
39: 130 type=165 (RBDIHS) 55 54 56 52
39: 131 type=165 (RBDIHS) 55 54 56 57
39: 132 type=155 (RBDIHS) 42 58 60 61
39: 133 type=156 (RBDIHS) 42 58 60 62
39: 134 type=155 (RBDIHS) 59 58 60 61
39: 135 type=157 (RBDIHS) 59 58 60 62
39: 136 type=159 (RBDIHS) 58 60 62 65
39: 137 type=150 (RBDIHS) 60 62 65 67
39: 138 type=155 (RBDIHS) 62 65 67 68
39: 139 type=156 (RBDIHS) 62 65 67 69
39: 140 type=155 (RBDIHS) 66 65 67 68
39: 141 type=157 (RBDIHS) 66 65 67 69
39: 142 type=158 (RBDIHS) 65 67 69 71
39: 143 type=159 (RBDIHS) 65 67 69 89
39: 144 type=166 (RBDIHS) 67 69 71 74
39: 145 type=167 (RBDIHS) 89 69 71 74
39: 146 type=147 (RBDIHS) 67 69 71 72
39: 147 type=147 (RBDIHS) 67 69 71 73
39: 148 type=148 (RBDIHS) 70 69 71 72
39: 149 type=148 (RBDIHS) 70 69 71 73
39: 150 type=148 (RBDIHS) 70 69 71 74
39: 151 type=149 (RBDIHS) 89 69 71 72
39: 152 type=149 (RBDIHS) 89 69 71 73
39: 153 type=150 (RBDIHS) 67 69 89 91
39: 154 type=151 (RBDIHS) 71 69 89 91
39: 155 type=148 (RBDIHS) 69 71 74 75
39: 156 type=148 (RBDIHS) 69 71 74 76
39: 157 type=152 (RBDIHS) 69 71 74 77
39: 158 type=148 (RBDIHS) 72 71 74 75
39: 159 type=148 (RBDIHS) 72 71 74 76
39: 160 type=148 (RBDIHS) 72 71 74 77
39: 161 type=148 (RBDIHS) 73 71 74 75
39: 162 type=148 (RBDIHS) 73 71 74 76
39: 163 type=148 (RBDIHS) 73 71 74 77
39: 164 type=148 (RBDIHS) 71 74 77 78
39: 165 type=148 (RBDIHS) 71 74 77 79
39: 166 type=153 (RBDIHS) 71 74 77 80
39: 167 type=148 (RBDIHS) 75 74 77 78
39: 168 type=148 (RBDIHS) 75 74 77 79
39: 169 type=168 (RBDIHS) 75 74 77 80
39: 170 type=148 (RBDIHS) 76 74 77 78
39: 171 type=148 (RBDIHS) 76 74 77 79
39: 172 type=168 (RBDIHS) 76 74 77 80
39: 173 type=169 (RBDIHS) 74 77 80 81
39: 174 type=170 (RBDIHS) 74 77 80 82
39: 175 type=171 (RBDIHS) 78 77 80 82
39: 176 type=171 (RBDIHS) 79 77 80 82
39: 177 type=172 (RBDIHS) 77 80 82 83
39: 178 type=172 (RBDIHS) 77 80 82 86
39: 179 type=173 (RBDIHS) 81 80 82 83
39: 180 type=173 (RBDIHS) 81 80 82 86
39: 181 type=173 (RBDIHS) 80 82 83 84
39: 182 type=173 (RBDIHS) 80 82 83 85
39: 183 type=173 (RBDIHS) 86 82 83 84
39: 184 type=173 (RBDIHS) 86 82 83 85
39: 185 type=173 (RBDIHS) 80 82 86 87
39: 186 type=173 (RBDIHS) 80 82 86 88
39: 187 type=173 (RBDIHS) 83 82 86 87
39: 188 type=173 (RBDIHS) 83 82 86 88
39: 189 type=155 (RBDIHS) 69 89 91 92
39: 190 type=156 (RBDIHS) 69 89 91 93
39: 191 type=155 (RBDIHS) 90 89 91 92
39: 192 type=157 (RBDIHS) 90 89 91 93
39: 193 type=158 (RBDIHS) 89 91 93 95
39: 194 type=159 (RBDIHS) 89 91 93 100
39: 195 type=174 (RBDIHS) 91 93 95 98
39: 196 type=175 (RBDIHS) 100 93 95 98
39: 197 type=147 (RBDIHS) 91 93 95 96
39: 198 type=147 (RBDIHS) 91 93 95 97
39: 199 type=148 (RBDIHS) 94 93 95 96
39: 200 type=148 (RBDIHS) 94 93 95 97
39: 201 type=176 (RBDIHS) 94 93 95 98
39: 202 type=149 (RBDIHS) 100 93 95 96
39: 203 type=149 (RBDIHS) 100 93 95 97
39: 204 type=150 (RBDIHS) 91 93 100 102
39: 205 type=151 (RBDIHS) 95 93 100 102
39: 206 type=177 (RBDIHS) 93 95 98 99
39: 207 type=178 (RBDIHS) 96 95 98 99
39: 208 type=178 (RBDIHS) 97 95 98 99
39: 209 type=155 (RBDIHS) 93 100 102 103
39: 210 type=156 (RBDIHS) 93 100 102 104
39: 211 type=155 (RBDIHS) 101 100 102 103
39: 212 type=157 (RBDIHS) 101 100 102 104
39: 213 type=158 (RBDIHS) 100 102 104 106
39: 214 type=159 (RBDIHS) 100 102 104 115
39: 215 type=179 (RBDIHS) 102 104 106 109
39: 216 type=180 (RBDIHS) 115 104 106 109
39: 217 type=147 (RBDIHS) 102 104 106 107
39: 218 type=147 (RBDIHS) 102 104 106 108
39: 219 type=148 (RBDIHS) 105 104 106 107
39: 220 type=148 (RBDIHS) 105 104 106 108
39: 221 type=148 (RBDIHS) 105 104 106 109
39: 222 type=149 (RBDIHS) 115 104 106 107
39: 223 type=149 (RBDIHS) 115 104 106 108
39: 224 type=150 (RBDIHS) 102 104 115 117
39: 225 type=151 (RBDIHS) 106 104 115 117
39: 226 type=148 (RBDIHS) 104 106 109 110
39: 227 type=148 (RBDIHS) 104 106 109 111
39: 228 type=181 (RBDIHS) 104 106 109 112
39: 229 type=148 (RBDIHS) 107 106 109 110
39: 230 type=148 (RBDIHS) 107 106 109 111
39: 231 type=182 (RBDIHS) 107 106 109 112
39: 232 type=148 (RBDIHS) 108 106 109 110
39: 233 type=148 (RBDIHS) 108 106 109 111
39: 234 type=182 (RBDIHS) 108 106 109 112
39: 235 type=183 (RBDIHS) 106 109 112 113
39: 236 type=183 (RBDIHS) 106 109 112 114
39: 237 type=155 (RBDIHS) 104 115 117 118
39: 238 type=156 (RBDIHS) 104 115 117 119
39: 239 type=155 (RBDIHS) 116 115 117 118
39: 240 type=157 (RBDIHS) 116 115 117 119
39: 241 type=158 (RBDIHS) 115 117 119 121
39: 242 type=159 (RBDIHS) 115 117 119 134
39: 243 type=184 (RBDIHS) 117 119 121 124
39: 244 type=185 (RBDIHS) 134 119 121 124
39: 245 type=147 (RBDIHS) 117 119 121 122
39: 246 type=147 (RBDIHS) 117 119 121 123
39: 247 type=148 (RBDIHS) 120 119 121 122
39: 248 type=148 (RBDIHS) 120 119 121 123
39: 249 type=148 (RBDIHS) 120 119 121 124
39: 250 type=149 (RBDIHS) 134 119 121 122
39: 251 type=149 (RBDIHS) 134 119 121 123
39: 252 type=150 (RBDIHS) 117 119 134 136
39: 253 type=151 (RBDIHS) 121 119 134 136
39: 254 type=148 (RBDIHS) 119 121 124 125
39: 255 type=152 (RBDIHS) 119 121 124 126
39: 256 type=152 (RBDIHS) 119 121 124 130
39: 257 type=148 (RBDIHS) 122 121 124 125
39: 258 type=148 (RBDIHS) 122 121 124 126
39: 259 type=148 (RBDIHS) 122 121 124 130
39: 260 type=148 (RBDIHS) 123 121 124 125
39: 261 type=148 (RBDIHS) 123 121 124 126
39: 262 type=148 (RBDIHS) 123 121 124 130
39: 263 type=148 (RBDIHS) 121 124 126 127
39: 264 type=148 (RBDIHS) 121 124 126 128
39: 265 type=148 (RBDIHS) 121 124 126 129
39: 266 type=148 (RBDIHS) 125 124 126 127
39: 267 type=148 (RBDIHS) 125 124 126 128
39: 268 type=148 (RBDIHS) 125 124 126 129
39: 269 type=148 (RBDIHS) 130 124 126 127
39: 270 type=148 (RBDIHS) 130 124 126 128
39: 271 type=148 (RBDIHS) 130 124 126 129
39: 272 type=148 (RBDIHS) 121 124 130 131
39: 273 type=148 (RBDIHS) 121 124 130 132
39: 274 type=148 (RBDIHS) 121 124 130 133
39: 275 type=148 (RBDIHS) 125 124 130 131
39: 276 type=148 (RBDIHS) 125 124 130 132
39: 277 type=148 (RBDIHS) 125 124 130 133
39: 278 type=148 (RBDIHS) 126 124 130 131
39: 279 type=148 (RBDIHS) 126 124 130 132
39: 280 type=148 (RBDIHS) 126 124 130 133
39: 281 type=155 (RBDIHS) 119 134 136 137
39: 282 type=156 (RBDIHS) 119 134 136 138
39: 283 type=155 (RBDIHS) 135 134 136 137
39: 284 type=157 (RBDIHS) 135 134 136 138
39: 285 type=158 (RBDIHS) 134 136 138 140
39: 286 type=159 (RBDIHS) 134 136 138 144
39: 287 type=147 (RBDIHS) 136 138 140 141
39: 288 type=147 (RBDIHS) 136 138 140 142
39: 289 type=147 (RBDIHS) 136 138 140 143
39: 290 type=148 (RBDIHS) 139 138 140 141
39: 291 type=148 (RBDIHS) 139 138 140 142
39: 292 type=148 (RBDIHS) 139 138 140 143
39: 293 type=149 (RBDIHS) 144 138 140 141
39: 294 type=149 (RBDIHS) 144 138 140 142
39: 295 type=149 (RBDIHS) 144 138 140 143
39: 296 type=150 (RBDIHS) 136 138 144 146
39: 297 type=151 (RBDIHS) 140 138 144 146
39: 298 type=155 (RBDIHS) 138 144 146 147
39: 299 type=156 (RBDIHS) 138 144 146 148
39: 300 type=155 (RBDIHS) 145 144 146 147
39: 301 type=157 (RBDIHS) 145 144 146 148
39: 302 type=158 (RBDIHS) 144 146 148 150
39: 303 type=159 (RBDIHS) 144 146 148 154
39: 304 type=147 (RBDIHS) 146 148 150 151
39: 305 type=147 (RBDIHS) 146 148 150 152
39: 306 type=147 (RBDIHS) 146 148 150 153
39: 307 type=148 (RBDIHS) 149 148 150 151
39: 308 type=148 (RBDIHS) 149 148 150 152
39: 309 type=148 (RBDIHS) 149 148 150 153
39: 310 type=149 (RBDIHS) 154 148 150 151
39: 311 type=149 (RBDIHS) 154 148 150 152
39: 312 type=149 (RBDIHS) 154 148 150 153
39: Restricted Dih.:
39: nr: 0
39: CBT Dih.:
39: nr: 0
39: Fourier Dih.:
39: nr: 0
39: Improper Dih.:
39: nr: 0
39: Improper Dih.:
39: nr: 0
39: Tab. Dih.:
39: nr: 0
39: CMAP Dih.:
39: nr: 0
39: GB 1-2 Pol. (unused):
39: nr: 0
39: GB 1-3 Pol. (unused):
39: nr: 0
39: GB 1-4 Pol. (unused):
39: nr: 0
39: GB Polarization (unused):
39: nr: 0
39: Nonpolar Sol. (unused):
39: nr: 0
39: LJ-14:
39: nr: 1197
39: iatoms:
39: 0 type=186 (LJ14) 0 7
39: 1 type=186 (LJ14) 0 8
39: 2 type=187 (LJ14) 0 9
39: 3 type=188 (LJ14) 0 23
39: 4 type=189 (LJ14) 0 24
39: 5 type=190 (LJ14) 1 5
39: 6 type=190 (LJ14) 1 6
39: 7 type=190 (LJ14) 1 22
39: 8 type=190 (LJ14) 2 5
39: 9 type=190 (LJ14) 2 6
39: 10 type=190 (LJ14) 2 22
39: 11 type=190 (LJ14) 3 5
39: 12 type=190 (LJ14) 3 6
39: 13 type=190 (LJ14) 3 22
39: 14 type=191 (LJ14) 4 10
39: 15 type=191 (LJ14) 4 11
39: 16 type=192 (LJ14) 4 12
39: 17 type=190 (LJ14) 4 25
39: 18 type=192 (LJ14) 4 26
39: 19 type=193 (LJ14) 5 7
39: 20 type=193 (LJ14) 5 8
39: 21 type=191 (LJ14) 5 9
39: 22 type=194 (LJ14) 5 23
39: 23 type=186 (LJ14) 5 24
39: 24 type=191 (LJ14) 6 13
39: 25 type=191 (LJ14) 6 14
39: 26 type=192 (LJ14) 6 15
39: 27 type=195 (LJ14) 6 23
39: 28 type=187 (LJ14) 6 24
39: 29 type=193 (LJ14) 7 10
39: 30 type=193 (LJ14) 7 11
39: 31 type=191 (LJ14) 7 12
39: 32 type=196 (LJ14) 7 22
39: 33 type=193 (LJ14) 8 10
39: 34 type=193 (LJ14) 8 11
39: 35 type=191 (LJ14) 8 12
39: 36 type=196 (LJ14) 8 22
39: 37 type=191 (LJ14) 9 16
39: 38 type=191 (LJ14) 9 17
39: 39 type=187 (LJ14) 9 18
39: 40 type=197 (LJ14) 9 22
39: 41 type=193 (LJ14) 10 13
39: 42 type=193 (LJ14) 10 14
39: 43 type=191 (LJ14) 10 15
39: 44 type=193 (LJ14) 11 13
39: 45 type=193 (LJ14) 11 14
39: 46 type=191 (LJ14) 11 15
39: 47 type=190 (LJ14) 12 19
39: 48 type=190 (LJ14) 12 20
39: 49 type=190 (LJ14) 12 21
39: 50 type=193 (LJ14) 13 16
39: 51 type=193 (LJ14) 13 17
39: 52 type=186 (LJ14) 13 18
39: 53 type=193 (LJ14) 14 16
39: 54 type=193 (LJ14) 14 17
39: 55 type=186 (LJ14) 14 18
39: 56 type=190 (LJ14) 16 19
39: 57 type=190 (LJ14) 16 20
39: 58 type=190 (LJ14) 16 21
39: 59 type=190 (LJ14) 17 19
39: 60 type=190 (LJ14) 17 20
39: 61 type=190 (LJ14) 17 21
39: 62 type=196 (LJ14) 22 27
39: 63 type=197 (LJ14) 22 28
39: 64 type=198 (LJ14) 22 38
39: 65 type=190 (LJ14) 23 25
39: 66 type=195 (LJ14) 23 26
39: 67 type=186 (LJ14) 24 29
39: 68 type=187 (LJ14) 24 30
39: 69 type=187 (LJ14) 24 34
39: 70 type=188 (LJ14) 24 39
39: 71 type=189 (LJ14) 24 40
39: 72 type=190 (LJ14) 25 27
39: 73 type=190 (LJ14) 25 28
39: 74 type=190 (LJ14) 25 38
39: 75 type=191 (LJ14) 26 31
39: 76 type=191 (LJ14) 26 32
39: 77 type=191 (LJ14) 26 33
39: 78 type=191 (LJ14) 26 35
39: 79 type=191 (LJ14) 26 36
39: 80 type=191 (LJ14) 26 37
39: 81 type=190 (LJ14) 26 41
39: 82 type=192 (LJ14) 26 42
39: 83 type=193 (LJ14) 27 29
39: 84 type=191 (LJ14) 27 30
39: 85 type=191 (LJ14) 27 34
39: 86 type=194 (LJ14) 27 39
39: 87 type=186 (LJ14) 27 40
39: 88 type=195 (LJ14) 28 39
39: 89 type=187 (LJ14) 28 40
39: 90 type=193 (LJ14) 29 31
39: 91 type=193 (LJ14) 29 32
39: 92 type=193 (LJ14) 29 33
39: 93 type=193 (LJ14) 29 35
39: 94 type=193 (LJ14) 29 36
39: 95 type=193 (LJ14) 29 37
39: 96 type=196 (LJ14) 29 38
39: 97 type=191 (LJ14) 30 35
39: 98 type=191 (LJ14) 30 36
39: 99 type=191 (LJ14) 30 37
39: 100 type=197 (LJ14) 30 38
39: 101 type=191 (LJ14) 31 34
39: 102 type=191 (LJ14) 32 34
39: 103 type=191 (LJ14) 33 34
39: 104 type=197 (LJ14) 34 38
39: 105 type=196 (LJ14) 38 43
39: 106 type=197 (LJ14) 38 44
39: 107 type=198 (LJ14) 38 58
39: 108 type=190 (LJ14) 39 41
39: 109 type=195 (LJ14) 39 42
39: 110 type=186 (LJ14) 40 45
39: 111 type=186 (LJ14) 40 46
39: 112 type=199 (LJ14) 40 47
39: 113 type=188 (LJ14) 40 59
39: 114 type=189 (LJ14) 40 60
39: 115 type=190 (LJ14) 41 43
39: 116 type=190 (LJ14) 41 44
39: 117 type=190 (LJ14) 41 58
39: 118 type=200 (LJ14) 42 48
39: 119 type=200 (LJ14) 42 50
39: 120 type=190 (LJ14) 42 61
39: 121 type=192 (LJ14) 42 62
39: 122 type=193 (LJ14) 43 45
39: 123 type=193 (LJ14) 43 46
39: 124 type=201 (LJ14) 43 47
39: 125 type=194 (LJ14) 43 59
39: 126 type=186 (LJ14) 43 60
39: 127 type=202 (LJ14) 44 49
39: 128 type=202 (LJ14) 44 51
39: 129 type=200 (LJ14) 44 52
39: 130 type=200 (LJ14) 44 54
39: 131 type=195 (LJ14) 44 59
39: 132 type=187 (LJ14) 44 60
39: 133 type=201 (LJ14) 45 48
39: 134 type=201 (LJ14) 45 50
39: 135 type=196 (LJ14) 45 58
39: 136 type=201 (LJ14) 46 48
39: 137 type=201 (LJ14) 46 50
39: 138 type=196 (LJ14) 46 58
39: 139 type=203 (LJ14) 47 53
39: 140 type=203 (LJ14) 47 55
39: 141 type=204 (LJ14) 47 56
39: 142 type=205 (LJ14) 47 58
39: 143 type=203 (LJ14) 48 51
39: 144 type=204 (LJ14) 48 54
39: 145 type=203 (LJ14) 48 57
39: 146 type=203 (LJ14) 49 50
39: 147 type=206 (LJ14) 49 53
39: 148 type=203 (LJ14) 49 56
39: 149 type=204 (LJ14) 50 52
39: 150 type=203 (LJ14) 50 57
39: 151 type=206 (LJ14) 51 55
39: 152 type=203 (LJ14) 51 56
39: 153 type=203 (LJ14) 52 55
39: 154 type=203 (LJ14) 53 54
39: 155 type=206 (LJ14) 53 57
39: 156 type=206 (LJ14) 55 57
39: 157 type=196 (LJ14) 58 63
39: 158 type=196 (LJ14) 58 64
39: 159 type=198 (LJ14) 58 65
39: 160 type=190 (LJ14) 59 61
39: 161 type=195 (LJ14) 59 62
39: 162 type=188 (LJ14) 60 66
39: 163 type=189 (LJ14) 60 67
39: 164 type=190 (LJ14) 61 63
39: 165 type=190 (LJ14) 61 64
39: 166 type=190 (LJ14) 61 65
39: 167 type=190 (LJ14) 62 68
39: 168 type=192 (LJ14) 62 69
39: 169 type=194 (LJ14) 63 66
39: 170 type=186 (LJ14) 63 67
39: 171 type=194 (LJ14) 64 66
39: 172 type=186 (LJ14) 64 67
39: 173 type=196 (LJ14) 65 70
39: 174 type=197 (LJ14) 65 71
39: 175 type=198 (LJ14) 65 89
39: 176 type=190 (LJ14) 66 68
39: 177 type=195 (LJ14) 66 69
39: 178 type=186 (LJ14) 67 72
39: 179 type=186 (LJ14) 67 73
39: 180 type=187 (LJ14) 67 74
39: 181 type=188 (LJ14) 67 90
39: 182 type=189 (LJ14) 67 91
39: 183 type=190 (LJ14) 68 70
39: 184 type=190 (LJ14) 68 71
39: 185 type=190 (LJ14) 68 89
39: 186 type=191 (LJ14) 69 75
39: 187 type=191 (LJ14) 69 76
39: 188 type=192 (LJ14) 69 77
39: 189 type=190 (LJ14) 69 92
39: 190 type=192 (LJ14) 69 93
39: 191 type=193 (LJ14) 70 72
39: 192 type=193 (LJ14) 70 73
39: 193 type=191 (LJ14) 70 74
39: 194 type=194 (LJ14) 70 90
39: 195 type=186 (LJ14) 70 91
39: 196 type=191 (LJ14) 71 78
39: 197 type=191 (LJ14) 71 79
39: 198 type=187 (LJ14) 71 80
39: 199 type=195 (LJ14) 71 90
39: 200 type=187 (LJ14) 71 91
39: 201 type=193 (LJ14) 72 75
39: 202 type=193 (LJ14) 72 76
39: 203 type=191 (LJ14) 72 77
39: 204 type=196 (LJ14) 72 89
39: 205 type=193 (LJ14) 73 75
39: 206 type=193 (LJ14) 73 76
39: 207 type=191 (LJ14) 73 77
39: 208 type=196 (LJ14) 73 89
39: 209 type=190 (LJ14) 74 81
39: 210 type=207 (LJ14) 74 82
39: 211 type=197 (LJ14) 74 89
39: 212 type=193 (LJ14) 75 78
39: 213 type=193 (LJ14) 75 79
39: 214 type=186 (LJ14) 75 80
39: 215 type=193 (LJ14) 76 78
39: 216 type=193 (LJ14) 76 79
39: 217 type=186 (LJ14) 76 80
39: 218 type=187 (LJ14) 77 83
39: 219 type=187 (LJ14) 77 86
39: 220 type=190 (LJ14) 78 81
39: 221 type=208 (LJ14) 78 82
39: 222 type=190 (LJ14) 79 81
39: 223 type=208 (LJ14) 79 82
39: 224 type=190 (LJ14) 80 84
39: 225 type=190 (LJ14) 80 85
39: 226 type=190 (LJ14) 80 87
39: 227 type=190 (LJ14) 80 88
39: 228 type=190 (LJ14) 81 83
39: 229 type=190 (LJ14) 81 86
39: 230 type=190 (LJ14) 83 87
39: 231 type=190 (LJ14) 83 88
39: 232 type=190 (LJ14) 84 86
39: 233 type=190 (LJ14) 85 86
39: 234 type=196 (LJ14) 89 94
39: 235 type=197 (LJ14) 89 95
39: 236 type=198 (LJ14) 89 100
39: 237 type=190 (LJ14) 90 92
39: 238 type=195 (LJ14) 90 93
39: 239 type=186 (LJ14) 91 96
39: 240 type=186 (LJ14) 91 97
39: 241 type=209 (LJ14) 91 98
39: 242 type=188 (LJ14) 91 101
39: 243 type=189 (LJ14) 91 102
39: 244 type=190 (LJ14) 92 94
39: 245 type=190 (LJ14) 92 95
39: 246 type=190 (LJ14) 92 100
39: 247 type=190 (LJ14) 93 99
39: 248 type=190 (LJ14) 93 103
39: 249 type=192 (LJ14) 93 104
39: 250 type=193 (LJ14) 94 96
39: 251 type=193 (LJ14) 94 97
39: 252 type=210 (LJ14) 94 98
39: 253 type=194 (LJ14) 94 101
39: 254 type=186 (LJ14) 94 102
39: 255 type=195 (LJ14) 95 101
39: 256 type=187 (LJ14) 95 102
39: 257 type=190 (LJ14) 96 99
39: 258 type=196 (LJ14) 96 100
39: 259 type=190 (LJ14) 97 99
39: 260 type=196 (LJ14) 97 100
39: 261 type=211 (LJ14) 98 100
39: 262 type=196 (LJ14) 100 105
39: 263 type=197 (LJ14) 100 106
39: 264 type=198 (LJ14) 100 115
39: 265 type=190 (LJ14) 101 103
39: 266 type=195 (LJ14) 101 104
39: 267 type=186 (LJ14) 102 107
39: 268 type=186 (LJ14) 102 108
39: 269 type=187 (LJ14) 102 109
39: 270 type=188 (LJ14) 102 116
39: 271 type=189 (LJ14) 102 117
39: 272 type=190 (LJ14) 103 105
39: 273 type=190 (LJ14) 103 106
39: 274 type=190 (LJ14) 103 115
39: 275 type=191 (LJ14) 104 110
39: 276 type=191 (LJ14) 104 111
39: 277 type=197 (LJ14) 104 112
39: 278 type=190 (LJ14) 104 118
39: 279 type=192 (LJ14) 104 119
39: 280 type=193 (LJ14) 105 107
39: 281 type=193 (LJ14) 105 108
39: 282 type=191 (LJ14) 105 109
39: 283 type=194 (LJ14) 105 116
39: 284 type=186 (LJ14) 105 117
39: 285 type=195 (LJ14) 106 113
39: 286 type=195 (LJ14) 106 114
39: 287 type=195 (LJ14) 106 116
39: 288 type=187 (LJ14) 106 117
39: 289 type=193 (LJ14) 107 110
39: 290 type=193 (LJ14) 107 111
39: 291 type=196 (LJ14) 107 112
39: 292 type=196 (LJ14) 107 115
39: 293 type=193 (LJ14) 108 110
39: 294 type=193 (LJ14) 108 111
39: 295 type=196 (LJ14) 108 112
39: 296 type=196 (LJ14) 108 115
39: 297 type=197 (LJ14) 109 115
39: 298 type=194 (LJ14) 110 113
39: 299 type=194 (LJ14) 110 114
39: 300 type=194 (LJ14) 111 113
39: 301 type=194 (LJ14) 111 114
39: 302 type=196 (LJ14) 115 120
39: 303 type=197 (LJ14) 115 121
39: 304 type=198 (LJ14) 115 134
39: 305 type=190 (LJ14) 116 118
39: 306 type=195 (LJ14) 116 119
39: 307 type=186 (LJ14) 117 122
39: 308 type=186 (LJ14) 117 123
39: 309 type=187 (LJ14) 117 124
39: 310 type=188 (LJ14) 117 135
39: 311 type=189 (LJ14) 117 136
39: 312 type=190 (LJ14) 118 120
39: 313 type=190 (LJ14) 118 121
39: 314 type=190 (LJ14) 118 134
39: 315 type=191 (LJ14) 119 125
39: 316 type=192 (LJ14) 119 126
39: 317 type=192 (LJ14) 119 130
39: 318 type=190 (LJ14) 119 137
39: 319 type=192 (LJ14) 119 138
39: 320 type=193 (LJ14) 120 122
39: 321 type=193 (LJ14) 120 123
39: 322 type=191 (LJ14) 120 124
39: 323 type=194 (LJ14) 120 135
39: 324 type=186 (LJ14) 120 136
39: 325 type=191 (LJ14) 121 127
39: 326 type=191 (LJ14) 121 128
39: 327 type=191 (LJ14) 121 129
39: 328 type=191 (LJ14) 121 131
39: 329 type=191 (LJ14) 121 132
39: 330 type=191 (LJ14) 121 133
39: 331 type=195 (LJ14) 121 135
39: 332 type=187 (LJ14) 121 136
39: 333 type=193 (LJ14) 122 125
39: 334 type=191 (LJ14) 122 126
39: 335 type=191 (LJ14) 122 130
39: 336 type=196 (LJ14) 122 134
39: 337 type=193 (LJ14) 123 125
39: 338 type=191 (LJ14) 123 126
39: 339 type=191 (LJ14) 123 130
39: 340 type=196 (LJ14) 123 134
39: 341 type=197 (LJ14) 124 134
39: 342 type=193 (LJ14) 125 127
39: 343 type=193 (LJ14) 125 128
39: 344 type=193 (LJ14) 125 129
39: 345 type=193 (LJ14) 125 131
39: 346 type=193 (LJ14) 125 132
39: 347 type=193 (LJ14) 125 133
39: 348 type=191 (LJ14) 126 131
39: 349 type=191 (LJ14) 126 132
39: 350 type=191 (LJ14) 126 133
39: 351 type=191 (LJ14) 127 130
39: 352 type=191 (LJ14) 128 130
39: 353 type=191 (LJ14) 129 130
39: 354 type=196 (LJ14) 134 139
39: 355 type=197 (LJ14) 134 140
39: 356 type=198 (LJ14) 134 144
39: 357 type=190 (LJ14) 135 137
39: 358 type=195 (LJ14) 135 138
39: 359 type=186 (LJ14) 136 141
39: 360 type=186 (LJ14) 136 142
39: 361 type=186 (LJ14) 136 143
39: 362 type=188 (LJ14) 136 145
39: 363 type=189 (LJ14) 136 146
39: 364 type=190 (LJ14) 137 139
39: 365 type=190 (LJ14) 137 140
39: 366 type=190 (LJ14) 137 144
39: 367 type=190 (LJ14) 138 147
39: 368 type=192 (LJ14) 138 148
39: 369 type=193 (LJ14) 139 141
39: 370 type=193 (LJ14) 139 142
39: 371 type=193 (LJ14) 139 143
39: 372 type=194 (LJ14) 139 145
39: 373 type=186 (LJ14) 139 146
39: 374 type=195 (LJ14) 140 145
39: 375 type=187 (LJ14) 140 146
39: 376 type=196 (LJ14) 141 144
39: 377 type=196 (LJ14) 142 144
39: 378 type=196 (LJ14) 143 144
39: 379 type=196 (LJ14) 144 149
39: 380 type=197 (LJ14) 144 150
39: 381 type=198 (LJ14) 144 154
39: 382 type=190 (LJ14) 145 147
39: 383 type=195 (LJ14) 145 148
39: 384 type=186 (LJ14) 146 151
39: 385 type=186 (LJ14) 146 152
39: 386 type=186 (LJ14) 146 153
39: 387 type=188 (LJ14) 146 155
39: 388 type=190 (LJ14) 147 149
39: 389 type=190 (LJ14) 147 150
39: 390 type=190 (LJ14) 147 154
39: 391 type=193 (LJ14) 149 151
39: 392 type=193 (LJ14) 149 152
39: 393 type=193 (LJ14) 149 153
39: 394 type=194 (LJ14) 149 155
39: 395 type=195 (LJ14) 150 155
39: 396 type=196 (LJ14) 151 154
39: 397 type=196 (LJ14) 152 154
39: 398 type=196 (LJ14) 153 154
39: Coulomb-14:
39: nr: 0
39: LJC-14 q:
39: nr: 0
39: LJC Pairs NB:
39: nr: 0
39: LJ (SR):
39: nr: 0
39: Buck.ham (SR):
39: nr: 0
39: LJ (unused):
39: nr: 0
39: B.ham (unused):
39: nr: 0
39: Disper. corr.:
39: nr: 0
39: Coulomb (SR):
39: nr: 0
39: Coul (unused):
39: nr: 0
39: RF excl.:
39: nr: 0
39: Coul. recip.:
39: nr: 0
39: LJ recip.:
39: nr: 0
39: DPD:
39: nr: 0
39: Polarization:
39: nr: 0
39: Water Pol.:
39: nr: 0
39: Thole Pol.:
39: nr: 0
39: Anharm. Pol.:
39: nr: 0
39: Position Rest.:
39: nr: 0
39: Flat-bottom posres:
39: nr: 0
39: Dis. Rest.:
39: nr: 0
39: D.R.Viol. (nm):
39: nr: 0
39: Orient. Rest.:
39: nr: 0
39: Ori. R. RMSD:
39: nr: 0
39: Angle Rest.:
39: nr: 0
39: Angle Rest. Z:
39: nr: 0
39: Dih. Rest.:
39: nr: 0
39: Dih. Rest. Viol.:
39: nr: 0
39: Constraint:
39: nr: 0
39: Constr. No Conn.:
39: nr: 0
39: Settle:
39: nr: 0
39: Virtual site 2:
39: nr: 0
39: Virtual site 2fd:
39: nr: 0
39: Virtual site 3:
39: nr: 0
39: Virtual site 3fd:
39: nr: 0
39: Virtual site 3fad:
39: nr: 0
39: Virtual site 3out:
39: nr: 0
39: Virtual site 4fd:
39: nr: 0
39: Virtual site 4fdn:
39: nr: 0
39: Virtual site N:
39: nr: 0
39: COM Pull En.:
39: nr: 0
39: Density fitting:
39: nr: 0
39: Quantum En.:
39: nr: 0
39: Potential:
39: nr: 0
39: Kinetic En.:
39: nr: 0
39: Total Energy:
39: nr: 0
39: Conserved En.:
39: nr: 0
39: Temperature:
39: nr: 0
39: Vir. Temp. (not used):
39: nr: 0
39: Pres. DC:
39: nr: 0
39: Pressure:
39: nr: 0
39: dH/dl constr.:
39: nr: 0
39: dVremain/dl:
39: nr: 0
39: dEkin/dl:
39: nr: 0
39: dVcoul/dl:
39: nr: 0
39: dVvdw/dl:
39: nr: 0
39: dVbonded/dl:
39: nr: 0
39: dVrestraint/dl:
39: nr: 0
39: dVtemperature/dl:
39: nr: 0
39: grp[T-Coupling ] nr=1, name=[ rest]
39: grp[Energy Mon. ] nr=1, name=[ rest]
39: grp[Acceleration] nr=1, name=[ rest]
39: grp[Freeze ] nr=1, name=[ rest]
39: grp[User1 ] nr=1, name=[ rest]
39: grp[User2 ] nr=1, name=[ rest]
39: grp[VCM ] nr=1, name=[ rest]
39: grp[Compressed X] nr=1, name=[ rest]
39: grp[Or. Res. Fit] nr=1, name=[ rest]
39: grp[QMMM ] nr=1, name=[ rest]
39: grpname (11):
39: grpname[0]={name="System"}
39: grpname[1]={name="Protein"}
39: grpname[2]={name="Protein-H"}
39: grpname[3]={name="C-alpha"}
39: grpname[4]={name="Backbone"}
39: grpname[5]={name="MainChain"}
39: grpname[6]={name="MainChain+Cb"}
39: grpname[7]={name="MainChain+H"}
39: grpname[8]={name="SideChain"}
39: grpname[9]={name="SideChain-H"}
39: grpname[10]={name="rest"}
39: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM
39: allocated 0 0 0 0 0 0 0 0 0 0
39: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0
39: box (3x3):
39: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00}
39: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00}
39: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00}
39: box_rel (3x3):
39: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: boxv (3x3):
39: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: pres_prev (3x3):
39: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: svir_prev (3x3):
39: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: fvir_prev (3x3):
39: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: nosehoover_xi: not available
39: x (156x3):
39: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00}
39: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00}
39: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00}
39: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00}
39: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00}
39: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00}
39: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00}
39: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00}
39: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01}
39: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01}
39: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01}
39: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00}
39: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01}
39: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01}
39: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01}
39: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01}
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39: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: Group statistics
39: T-Coupling : 156 (total 156 atoms)
39: Energy Mon. : 156 (total 156 atoms)
39: Acceleration: 156 (total 156 atoms)
39: Freeze : 156 (total 156 atoms)
39: User1 : 156 (total 156 atoms)
39: User2 : 156 (total 156 atoms)
39: VCM : 156 (total 156 atoms)
39: Compressed X: 156 (total 156 atoms)
39: Or. Res. Fit: 156 (total 156 atoms)
39: QMMM : 156 (total 156 atoms)
39: [ OK ] DumpTest.WorksWithTpr (77 ms)
39: [ RUN ] DumpTest.WorksWithTprAndMdpWriting
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
39: [ OK ] DumpTest.WorksWithTprAndMdpWriting (3 ms)
39: [----------] 2 tests from DumpTest (80 ms total)
39:
39: [----------] 4 tests from ReportMethodsTest
39:
39: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
39: For a correct single-point energy evaluation with nsteps = 0, use
39: continuation = yes to avoid constraining the input coordinates.
39:
39: Setting the LD random seed to -1343357590
39: Generated 330891 of the 330891 non-bonded parameter combinations
39: Generating 1-4 interactions: fudge = 0.5
39: Generated 330891 of the 330891 1-4 parameter combinations
39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
39:
39: NOTE 2 [file lysozyme.top, line 1465]:
39: System has non-zero total charge: 2.000000
39: Total charge should normally be an integer. See
39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
39: for discussion on how close it should be to an integer.
39:
39:
39:
39: Number of degrees of freedom in T-Coupling group rest is 465.00
39:
39: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
39: NVE simulation with an initial temperature of zero: will use a Verlet
39: buffer of 10%. Check your energy drift!
39:
39:
39: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
39: You are using a plain Coulomb cut-off, which might produce artifacts.
39: You might want to consider using PME electrostatics.
39:
39:
39:
39: There were 4 notes
39: Analysing residue names:
39: There are: 10 Protein residues
39: Analysing Protein...
39: This run will generate roughly 0 Mb of data
39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
39: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms)
39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
39: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms)
39: [ RUN ] ReportMethodsTest.WritesCorrectInformation
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
39: [ OK ] ReportMethodsTest.WritesCorrectInformation (1 ms)
39: [ RUN ] ReportMethodsTest.ToolEndToEndTest
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
39: section: Methods
39: subsection: Simulation system
39: A system of 1 molecules (156 atoms) was simulated.
39:
39: subsection: Simulation settings
39: A total of 0 ns were simulated with a time step of 1 fs.
39: Neighbor searching was performed every 10 steps.
39: The Cut-off algorithm was used for electrostatic interactions.
39: with a cut-off of 1 nm.
39: A single cut-off of 1.1 nm was used for Van der Waals interactions.
39: [ OK ] ReportMethodsTest.ToolEndToEndTest (1 ms)
39: [----------] 4 tests from ReportMethodsTest (4 ms total)
39:
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: trr version: GMX_trn_file (single precision)
39:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (6 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (7 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (5 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from gro file '', 6 atoms.
39:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (5 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
39: -> frame 0 time 0.000
't= 0.00000', 6 atoms
39:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (4 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (5 ms)
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (34 ms total)
39:
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (2 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (3 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (2 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from gro file '', 6 atoms.
39:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (2 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
39: -> frame 0 time 0.000
't= 0.00000', 6 atoms
39:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (2 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (2 ms)
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (13 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 18 tests from 4 test cases ran. (2063 ms total)
39: [ PASSED ] 18 tests.
39/54 Test #39: ToolUnitTests ....................... Passed 2.09 sec
test 40
Start 40: FileIOTests
40: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FileIOTests.xml"
40: Test timeout computed to be: 30
40: [==========] Running 33 tests from 8 test cases.
40: [----------] Global test environment set-up.
40: [----------] 2 tests from FileMD5Test
40: [ RUN ] FileMD5Test.CanComputeMD5
40: [ OK ] FileMD5Test.CanComputeMD5 (1 ms)
40: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
40: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms)
40: [----------] 2 tests from FileMD5Test (2 ms total)
40:
40: [----------] 3 tests from MrcSerializer
40: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet
40: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms)
40: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize
40: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms)
40: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip
40: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (6 ms)
40: [----------] 3 tests from MrcSerializer (6 ms total)
40:
40: [----------] 4 tests from MrcDensityMap
40: [ RUN ] MrcDensityMap.RoundTripIsIdempotent
40: [ OK ] MrcDensityMap.RoundTripIsIdempotent (5 ms)
40: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent
40: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (1 ms)
40: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile
40: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms)
40: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile
40: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (2 ms)
40: [----------] 4 tests from MrcDensityMap (8 ms total)
40:
40: [----------] 8 tests from MrcDensityMapHeaderTest
40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader
40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect
40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid
40: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.IsSane
40: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms)
40: [----------] 8 tests from MrcDensityMapHeaderTest (1 ms total)
40:
40: [----------] 9 tests from ReadTest
40: [ RUN ] ReadTest.get_eint_ReadsInteger
40: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
40: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side '0.8' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms)
40: [ RUN ] ReadTest.get_eint_WarnsAboutString
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side 'hello' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
40: [ RUN ] ReadTest.get_eint64_ReadsInteger
40: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
40: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side '0.8' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms)
40: [ RUN ] ReadTest.get_eint64_WarnsAboutString
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side 'hello' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
40: [ RUN ] ReadTest.get_ereal_ReadsInteger
40: [ OK ] ReadTest.get_ereal_ReadsInteger (1 ms)
40: [ RUN ] ReadTest.get_ereal_ReadsFloat
40: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
40: [ RUN ] ReadTest.get_ereal_WarnsAboutString
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side 'hello' for parameter 'test' in parameter file is not a
40: real value
40:
40:
40: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
40: [----------] 9 tests from ReadTest (1 ms total)
40:
40: [----------] 1 test from FileIOXdrSerializerTest
40: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect
40: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms)
40: [----------] 1 test from FileIOXdrSerializerTest (0 ms total)
40:
40: [----------] 2 tests from TngTest
40: [ RUN ] TngTest.CanOpenTngFile
40: TNG library: Cannot open file spc2-traj.tng. /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: 890
40: TNG library: Cannot open file spc2-traj.tng. /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: 890
40: [ OK ] TngTest.CanOpenTngFile (0 ms)
40: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
40: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
40: [----------] 2 tests from TngTest (1 ms total)
40:
40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (1 ms)
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms)
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (5 ms)
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms)
40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (8 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 33 tests from 8 test cases ran. (27 ms total)
40: [ PASSED ] 33 tests.
40/54 Test #40: FileIOTests ......................... Passed 0.05 sec
test 41
Start 41: SelectionUnitTests
41: Test command: /<<PKGBUILDDIR>>/build/basic/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SelectionUnitTests.xml"
41: Test timeout computed to be: 30
41: [==========] Running 192 tests from 11 test cases.
41: [----------] Global test environment set-up.
41: [----------] 1 test from IndexGroupTest
41: [ RUN ] IndexGroupTest.RemovesDuplicates
41: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
41: [----------] 1 test from IndexGroupTest (0 ms total)
41:
41: [----------] 15 tests from IndexBlockTest
41: [ RUN ] IndexBlockTest.CreatesUnknownBlock
41: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms)
41: [ RUN ] IndexBlockTest.CreatesAtomBlock
41: [ OK ] IndexBlockTest.CreatesAtomBlock (1 ms)
41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology
41: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms)
41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology
41: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (1 ms)
41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology
41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms)
41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology
41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms)
41: [ RUN ] IndexBlockTest.CreatesSingleBlock
41: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
41: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (1 ms)
41: [----------] 15 tests from IndexBlockTest (4 ms total)
41:
41: [----------] 11 tests from IndexMapTest
41: [ RUN ] IndexMapTest.InitializesAtomBlock
41: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
41: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
41: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
41: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
41: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
41: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms)
41: [ RUN ] IndexMapTest.InitializesMoleculeBlock
41: [ OK ] IndexMapTest.InitializesMoleculeBlock (1 ms)
41: [ RUN ] IndexMapTest.MapsSingleBlock
41: [ OK ] IndexMapTest.MapsSingleBlock (0 ms)
41: [ RUN ] IndexMapTest.MapsResidueBlocks
41: [ OK ] IndexMapTest.MapsResidueBlocks (0 ms)
41: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
41: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms)
41: [ RUN ] IndexMapTest.HandlesMultipleRequests
41: [ OK ] IndexMapTest.HandlesMultipleRequests (1 ms)
41: [----------] 11 tests from IndexMapTest (4 ms total)
41:
41: [----------] 3 tests from IndexGroupsAndNamesTest
41: [ RUN ] IndexGroupsAndNamesTest.containsNames
41: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms)
41: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing
41: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms)
41: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect
41: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (1 ms)
41: [----------] 3 tests from IndexGroupsAndNamesTest (1 ms total)
41:
41: [----------] 15 tests from NeighborhoodSearchTest
41: [ RUN ] NeighborhoodSearchTest.SimpleSearch
41: [ OK ] NeighborhoodSearchTest.SimpleSearch (35 ms)
41: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
41: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (32 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchBox
41: [ OK ] NeighborhoodSearchTest.GridSearchBox (5 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
41: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (23 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
41: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (10 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
41: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (5 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
41: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (4 ms)
41: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
41: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (1 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
41: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (95 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
41: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
41: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
41: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
41: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms)
41: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
41: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (7 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
41: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (2 ms)
41: [----------] 15 tests from NeighborhoodSearchTest (220 ms total)
41:
41: [----------] 12 tests from PositionCalculationTest
41: [ RUN ] PositionCalculationTest.ComputesAtomPositions
41: [ OK ] PositionCalculationTest.ComputesAtomPositions (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
41: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms)
41: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
41: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
41: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms)
41: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
41: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms)
41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms)
41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms)
41: [ RUN ] PositionCalculationTest.ComputesPositionMask
41: [ OK ] PositionCalculationTest.ComputesPositionMask (1 ms)
41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms)
41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (1 ms)
41: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
41: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (0 ms)
41: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
41: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms)
41: [----------] 12 tests from PositionCalculationTest (6 ms total)
41:
41: [----------] 29 tests from SelectionCollectionTest
41: [ RUN ] SelectionCollectionTest.HandlesNoSelections
41: [ OK ] SelectionCollectionTest.HandlesNoSelections (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
41: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
41: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
41: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (2 ms)
41: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
41: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms)
41: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
41: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
41: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms)
41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
41: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (2 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
41: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
41: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (2 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (3 ms)
41: [----------] 29 tests from SelectionCollectionTest (36 ms total)
41:
41: [----------] 14 tests from SelectionCollectionInteractiveTest
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
41: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (3 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
41: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms)
41: [----------] 14 tests from SelectionCollectionInteractiveTest (23 ms total)
41:
41: [----------] 66 tests from SelectionCollectionDataTest
41: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
41: [ OK ] SelectionCollectionDataTest.HandlesAllNone (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
41: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesResnr
41: [ OK ] SelectionCollectionDataTest.HandlesResnr (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
41: [ OK ] SelectionCollectionDataTest.HandlesResIndex (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
41: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
41: [ OK ] SelectionCollectionDataTest.HandlesAtomname (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
41: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
41: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesChain
41: [ OK ] SelectionCollectionDataTest.HandlesChain (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMass
41: [ OK ] SelectionCollectionDataTest.HandlesMass (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesCharge
41: [ OK ] SelectionCollectionDataTest.HandlesCharge (1 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
41: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
41: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
41: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBeta
41: [ OK ] SelectionCollectionDataTest.HandlesBeta (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesResname
41: [ OK ] SelectionCollectionDataTest.HandlesResname (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
41: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
41: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
41: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
41: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (9 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (16 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
41: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
41: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (12 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
41: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (13 ms)
41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (6 ms)
41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
41: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
41: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (1 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (1 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
41: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (1 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
41: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
41: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
41: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
41: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (9 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
41: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
41: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
41: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
41: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (7 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
41: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (9 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
41: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
41: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (10 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (7 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
41: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (12 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
41: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (5 ms)
41: [----------] 66 tests from SelectionCollectionDataTest (323 ms total)
41:
41: [----------] 17 tests from SelectionOptionTest
41: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
41: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms)
41: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
41: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
41: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (2 ms)
41: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
41: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (2 ms)
41: [ RUN ] SelectionOptionTest.ChecksEmptySelections
41: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms)
41: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
41: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooManySelections
41: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
41: [ OK ] SelectionOptionTest.HandlesTooFewSelections (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
41: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesAdjuster
41: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms)
41: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms)
41: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
41: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
41: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms)
41: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
41: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms)
41: [----------] 17 tests from SelectionOptionTest (13 ms total)
41:
41: [----------] 9 tests from SelectionFileOptionTest
41: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
41: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
41: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
41: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
41: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (0 ms)
41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
41: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
41: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (0 ms)
41: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
41: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (1 ms)
41: [----------] 9 tests from SelectionFileOptionTest (7 ms total)
41:
41: [----------] Global test environment tear-down
41: [==========] 192 tests from 11 test cases ran. (637 ms total)
41: [ PASSED ] 192 tests.
41/54 Test #41: SelectionUnitTests .................. Passed 0.67 sec
test 42
Start 42: MdrunOutputTests
42: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunOutputTests.xml"
42: Test timeout computed to be: 600
42: [==========] Running 12 tests from 5 test cases.
42: [----------] Global test environment set-up.
42: [----------] 1 test from MdrunTest
42: [ RUN ] MdrunTest.WritesHelp
42: [ OK ] MdrunTest.WritesHelp (4 ms)
42: [----------] 1 test from MdrunTest (5 ms total)
42:
42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
42: Setting the LD random seed to -1278427391
42: Generated 3 of the 3 non-bonded parameter combinations
42: Generating 1-4 interactions: fudge = 0.5
42: Generated 3 of the 3 1-4 parameter combinations
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group rest is 9.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
42: NVE simulation: will use the initial temperature of 2573.591 K for
42: determining the Verlet buffer size
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There were 2 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc2'
42: 1 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.204 0.102 199.4
42: (ns/day) (hour/ns)
42: Performance: 1.692 14.185
42:
Reading frame 0 time 0.000
42: # Atoms 6
42:
Reading frame 1 time 0.001
Last frame 1 time 0.001
42:
42:
42: Item #frames Timestep (ps)
42: Step 2 0.001
42: Time 2 0.001
42: Lambda 0
42: Coords 2 0.001
42: Velocities 0
42: Forces 0
42: Box 2 0.001
42: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (144 ms)
42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
42: Setting the LD random seed to 1657577854
42: Generated 3 of the 3 non-bonded parameter combinations
42: Generating 1-4 interactions: fudge = 0.5
42: Generated 3 of the 3 1-4 parameter combinations
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group rest is 9.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
42: NVE simulation: will use the initial temperature of 2573.591 K for
42: determining the Verlet buffer size
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There were 2 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc2'
42: 1 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.155 0.078 199.2
42: (ns/day) (hour/ns)
42: Performance: 2.221 10.808
42:
Reading frame 0 time 0.000
42: # Atoms 6
42:
Reading frame 1 time 0.001
Last frame 1 time 0.001
42:
42:
42: Item #frames Timestep (ps)
42: Step 2 0.001
42: Time 2 0.001
42: Lambda 0
42: Coords 2 0.001
42: Velocities 0
42: Forces 0
42: Box 2 0.001
42: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (100 ms)
42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
42: Setting the LD random seed to -1365797612
42: Generated 3 of the 3 non-bonded parameter combinations
42: Generating 1-4 interactions: fudge = 0.5
42: Generated 3 of the 3 1-4 parameter combinations
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group rest is 9.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
42: NVE simulation: will use the initial temperature of 2573.591 K for
42: determining the Verlet buffer size
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There were 2 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc2'
42: 1 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.189 0.095 199.4
42: (ns/day) (hour/ns)
42: Performance: 1.826 13.146
42:
Reading frame 0 time 0.000
42: # Atoms 3
42:
Reading frame 1 time 0.001
Last frame 1 time 0.001
42:
42:
42: Item #frames Timestep (ps)
42: Step 2 0.001
42: Time 2 0.001
42: Lambda 0
42: Coords 2 0.001
42: Velocities 0
42: Forces 0
42: Box 2 0.001
42: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (117 ms)
42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (361 ms total)
42:
42: [----------] 2 tests from Argon12/OutputFiles
42: [ RUN ] Argon12/OutputFiles.FilesArePresent/0
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
42: that with the Verlet scheme, nstlist has no effect on the accuracy of
42: your simulation.
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
42: Setting nstcalcenergy (100) equal to nstenergy (4)
42:
42: Generated 1 of the 1 non-bonded parameter combinations
42: Excluding 1 bonded neighbours molecule type 'Argon'
42: Number of degrees of freedom in T-Coupling group System is 33.00
42:
42: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
42: NVE simulation: will use the initial temperature of 68.810 K for
42: determining the Verlet buffer size
42:
42:
42: There were 3 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'Argon'
42: 16 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.189 0.095 199.4
42: (ns/day) (hour/ns)
42: Performance: 15.479 1.551
42: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (116 ms)
42: [ RUN ] Argon12/OutputFiles.FilesArePresent/1
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
42: that with the Verlet scheme, nstlist has no effect on the accuracy of
42: your simulation.
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
42: Setting nstcalcenergy (100) equal to nstenergy (4)
42:
42: Generated 1 of the 1 non-bonded parameter combinations
42: Excluding 1 bonded neighbours molecule type 'Argon'
42: Number of degrees of freedom in T-Coupling group System is 33.00
42:
42: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
42: NVE simulation: will use the initial temperature of 68.810 K for
42: determining the Verlet buffer size
42:
42:
42: There were 3 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'Argon'
42: 16 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.176 0.088 199.5
42: (ns/day) (hour/ns)
42: Performance: 16.655 1.441
42: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (108 ms)
42: [----------] 2 tests from Argon12/OutputFiles (224 ms total)
42:
42: [----------] 3 tests from MdrunCanWrite/Trajectories
42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
42: Setting the LD random seed to 176726161
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 6 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.134 0.067 199.0
42: (ns/day) (hour/ns)
42: Performance: 9.003 2.666
42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (92 ms)
42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
42: Setting the LD random seed to 162657242
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 6 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.133 0.067 199.0
42: (ns/day) (hour/ns)
42: Performance: 9.065 2.648
42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (91 ms)
42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
42: Setting the LD random seed to -511091952
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 6 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.134 0.067 199.0
42: (ns/day) (hour/ns)
42: Performance: 9.004 2.666
42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (92 ms)
42: [----------] 3 tests from MdrunCanWrite/Trajectories (275 ms total)
42:
42: [----------] 3 tests from MdrunCanWrite/NptTrajectories
42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
42: Setting the LD random seed to 1267746902
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 2 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.118 0.059 198.9
42: (ns/day) (hour/ns)
42: Performance: 4.365 5.499
42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (83 ms)
42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
42: Setting the LD random seed to -465194743
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 2 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.134 0.067 198.9
42: (ns/day) (hour/ns)
42: Performance: 3.849 6.235
42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (92 ms)
42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
42: Setting the LD random seed to -93826780
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 2 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.118 0.059 198.8
42: (ns/day) (hour/ns)
42: Performance: 4.360 5.505
42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (83 ms)
42: [----------] 3 tests from MdrunCanWrite/NptTrajectories (258 ms total)
42:
42: [----------] Global test environment tear-down
42: [==========] 12 tests from 5 test cases ran. (1124 ms total)
42: [ PASSED ] 12 tests.
42/54 Test #42: MdrunOutputTests .................... Passed 1.15 sec
test 43
Start 43: MdrunModulesTests
43: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunModulesTests.xml"
43: Test timeout computed to be: 600
43: [==========] Running 10 tests from 3 test cases.
43: [----------] Global test environment set-up.
43: [----------] 4 tests from DensityFittingTest
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct
43: Setting the LD random seed to -951492271
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -3.8565400e+03
43: Maximum force = 2.8846870e+03 on atom 3
43: Norm of force = 1.0754448e+03
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (45 ms)
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy
43: Setting the LD random seed to -1208772182
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -2.7138666e+04
43: Maximum force = 4.3409717e+03 on atom 2
43: Norm of force = 1.2549793e+03
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (26 ms)
43: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch
43:
43: [WARNING] /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-death-test.cc:836:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads.
43: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (17 ms)
43: [ RUN ] DensityFittingTest.CheckpointWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (2)
43:
43: Setting the LD random seed to -420617041
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.131 0.066 199.2
43: (ns/day) (hour/ns)
43: Performance: 3.937 6.095
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
43: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps
43: Can not increase nstlist because an NVE ensemble is used
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.164 0.082 199.4
43: (ns/day) (hour/ns)
43: Performance: 5.251 4.570
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (180 ms)
43: [----------] 4 tests from DensityFittingTest (268 ms total)
43:
43: [----------] 4 tests from MimicTest
43: [ RUN ] MimicTest.OneQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1636478964
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.002 0.001 175.3
43: (ns/day) (hour/ns)
43: Performance: 98.288 0.244
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.OneQuantumMol (23 ms)
43: [ RUN ] MimicTest.AllQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 628971430
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.002 0.001 173.7
43: (ns/day) (hour/ns)
43: Performance: 98.502 0.244
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.AllQuantumMol (22 ms)
43: [ RUN ] MimicTest.TwoQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1596567870
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.001 0.001 173.9
43: (ns/day) (hour/ns)
43: Performance: 100.972 0.238
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.TwoQuantumMol (22 ms)
43: [ RUN ] MimicTest.BondCuts
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -549530559
43: Generated 2211 of the 2211 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2211 of the 2211 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
43: Number of degrees of freedom in T-Coupling group rest is 66.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: NVE simulation: will use the initial temperature of 300.368 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
43:
43: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.002 0.001 183.5
43: (ns/day) (hour/ns)
43: Performance: 64.060 0.375
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
43: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.BondCuts (68 ms)
43: [----------] 4 tests from MimicTest (135 ms total)
43:
43: [----------] 2 tests from WithIntegrator/ImdTest
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0
43: Setting the LD random seed to -833565112
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43:
43: NOTE 1 [file glycine_vacuo.top, line 12]:
43: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an
43: estimated oscillational period of 1.0e-02 ps, which is less than 10 times
43: the time step of 2.0e-03 ps.
43: Maybe you forgot to change the constraints mdp option.
43:
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
43: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 49145.
43: IMD: -imdwait not set, starting simulation.
43: starting mdrun 'Glycine'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.188 0.095 199.2
43: (ns/day) (hour/ns)
43: Performance: 5.485 4.376
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (531 ms)
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not
43: apply to steep.
43:
43: Setting the LD random seed to 1743069906
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 51195.
43: IMD: -imdwait not set, starting simulation.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = 1.1977063e+03
43: Maximum force = 1.7794877e+04 on atom 9
43: Norm of force = 7.8732901e+03
43: This run will generate roughly 0 Mb of data
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (435 ms)
43: [----------] 2 tests from WithIntegrator/ImdTest (966 ms total)
43:
43: [----------] Global test environment tear-down
43: [==========] 10 tests from 3 test cases ran. (1369 ms total)
43: [ PASSED ] 10 tests.
43/54 Test #43: MdrunModulesTests ................... Passed 1.39 sec
test 44
Start 44: MdrunIOTests
44: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunIOTests.xml"
44: Test timeout computed to be: 600
44: [==========] Running 51 tests from 9 test cases.
44: [----------] Global test environment set-up.
44: [----------] 3 tests from GromppTest
44: [ RUN ] GromppTest.EmptyMdpFileWorks
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
44: For a correct single-point energy evaluation with nsteps = 0, use
44: continuation = yes to avoid constraining the input coordinates.
44:
44: Setting the LD random seed to -180576958
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 12.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
44: NVE simulation: will use the initial temperature of 1046.791 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: [ OK ] GromppTest.EmptyMdpFileWorks (10 ms)
44: [ RUN ] GromppTest.SimulatedAnnealingWorks
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
44: For a correct single-point energy evaluation with nsteps = 0, use
44: continuation = yes to avoid constraining the input coordinates.
44:
44: Setting the LD random seed to 2033162762
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Simulated annealing for group rest: Periodic, 4 timepoints
44: Time (ps) Temperature (K)
44: 0.0 298.0
44: 2.0 320.0
44: 4.0 320.0
44: 6.0 298.0
44: Number of degrees of freedom in T-Coupling group rest is 12.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
44: NVE simulation: will use the initial temperature of 1046.791 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: [ OK ] GromppTest.SimulatedAnnealingWorks (9 ms)
44: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
44: For a correct single-point energy evaluation with nsteps = 0, use
44: continuation = yes to avoid constraining the input coordinates.
44:
44: Setting the LD random seed to 781556804
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Simulated annealing for group Methanol: Single, 3 timepoints
44: Time (ps) Temperature (K)
44: 0.0 298.0
44: 3.0 280.0
44: 6.0- 270.0
44: Simulated annealing for group SOL: Periodic, 4 timepoints
44: Time (ps) Temperature (K)
44: 0.0 298.0
44: 2.0 320.0
44: 4.0 320.0
44: 6.0 298.0
44: Number of degrees of freedom in T-Coupling group Methanol is 7.20
44: Number of degrees of freedom in T-Coupling group SOL is 4.80
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
44: NVE simulation: will use the initial temperature of 1046.791 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (10 ms)
44: [----------] 3 tests from GromppTest (29 ms total)
44:
44: [----------] 6 tests from MdrunTerminationTest
44: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault
44: Setting the LD random seed to 524759656
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.155 0.078 199.3
44: (ns/day) (hour/ns)
44: Performance: 3.324 7.220
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.113 0.057 199.1
44: (ns/day) (hour/ns)
44: Performance: 4.586 5.233
44: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (187 ms)
44: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
44: Setting the LD random seed to 622922439
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 10 to 1, rlist from 1.024 to 1
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 100 steps, 0.1 ps.
44:
44: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.102 0.052 198.9
44: (ns/day) (hour/ns)
44: Performance: 5.031 4.771
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Setting nsteps to 102
44: Writing statusfile with starting step 0 and length 102 steps...
44: time 0.000 and length 0.102 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 102 steps, 0.1 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.147 0.074 199.2
44: (ns/day) (hour/ns)
44: Performance: 118.559 0.202
44: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (158 ms)
44: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend
44: Setting the LD random seed to 1263067376
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.120 0.060 199.1
44: (ns/day) (hour/ns)
44: Performance: 4.302 5.579
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.129 0.065 199.5
44: (ns/day) (hour/ns)
44: Performance: 4.010 5.985
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Setting nsteps to 6
44: Writing statusfile with starting step 0 and length 6 steps...
44: time 0.000 and length 0.006 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.157 0.079 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.299 7.275
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Setting nsteps to 8
44: Writing statusfile with starting step 0 and length 8 steps...
44: time 0.000 and length 0.008 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.145 0.073 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.557 6.748
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.001 0.001 155.9
44: (ns/day) (hour/ns)
44: Performance: 124.190 0.193
44: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (343 ms)
44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile
44: Setting the LD random seed to -1437796012
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.152 0.076 199.3
44: (ns/day) (hour/ns)
44: Performance: 3.400 7.060
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.130 0.065 199.1
44: (ns/day) (hour/ns)
44: Performance: 6.620 3.625
44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (174 ms)
44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile
44: Setting the LD random seed to -1239201962
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.120 0.060 199.1
44: (ns/day) (hour/ns)
44: Performance: 4.298 5.585
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (85 ms)
44: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles
44: Setting the LD random seed to -1676371643
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.100 0.050 198.9
44: (ns/day) (hour/ns)
44: Performance: 5.151 4.660
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.171 0.086 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.027 7.929
44: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (168 ms)
44: [----------] 6 tests from MdrunTerminationTest (1115 ms total)
44:
44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.572 0.286 199.8
44: (ns/day) (hour/ns)
44: Performance: 5.127 4.681
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.218 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.125 3.368
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.199 0.100 199.5
44: (ns/day) (hour/ns)
44: Performance: 7.798 3.078
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (550 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.174 0.087 199.5
44: (ns/day) (hour/ns)
44: Performance: 16.800 1.429
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.202 0.101 199.6
44: (ns/day) (hour/ns)
44: Performance: 7.667 3.130
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.184 0.092 199.6
44: (ns/day) (hour/ns)
44: Performance: 8.446 2.841
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (333 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.222 0.111 199.5
44: (ns/day) (hour/ns)
44: Performance: 13.193 1.819
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.201 0.101 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.713 3.112
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.5
44: (ns/day) (hour/ns)
44: Performance: 7.211 3.328
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (375 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.205 0.103 199.5
44: (ns/day) (hour/ns)
44: Performance: 14.279 1.681
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.144 3.360
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.165 0.083 199.4
44: (ns/day) (hour/ns)
44: Performance: 9.383 2.558
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (350 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.203 0.102 199.4
44: (ns/day) (hour/ns)
44: Performance: 14.450 1.661
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.251 0.126 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.189 3.878
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.249 0.125 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.239 3.847
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (408 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.222 0.111 199.6
44: (ns/day) (hour/ns)
44: Performance: 13.235 1.813
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.169 0.085 199.4
44: (ns/day) (hour/ns)
44: Performance: 9.198 2.609
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.167 0.084 199.5
44: (ns/day) (hour/ns)
44: Performance: 9.311 2.578
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (333 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.202 0.101 199.4
44: (ns/day) (hour/ns)
44: Performance: 14.487 1.657
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.216 0.108 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.173 3.346
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.248 0.124 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.263 3.832
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (392 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.186 0.093 199.3
44: (ns/day) (hour/ns)
44: Performance: 15.729 1.526
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.133 0.067 199.0
44: (ns/day) (hour/ns)
44: Performance: 11.621 2.065
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.148 0.074 199.2
44: (ns/day) (hour/ns)
44: Performance: 10.462 2.294
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (291 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.206 0.103 199.3
44: (ns/day) (hour/ns)
44: Performance: 14.198 1.690
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.263 0.132 199.4
44: (ns/day) (hour/ns)
44: Performance: 5.890 4.075
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.228 0.115 199.3
44: (ns/day) (hour/ns)
44: Performance: 6.785 3.537
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (502 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.206 0.103 199.3
44: (ns/day) (hour/ns)
44: Performance: 14.203 1.690
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.164 0.082 198.9
44: (ns/day) (hour/ns)
44: Performance: 9.438 2.543
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.195 0.098 199.2
44: (ns/day) (hour/ns)
44: Performance: 7.955 3.017
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (433 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.272 0.136 199.3
44: (ns/day) (hour/ns)
44: Performance: 10.784 2.226
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.198 0.099 199.2
44: (ns/day) (hour/ns)
44: Performance: 7.832 3.064
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.245 0.123 199.3
44: (ns/day) (hour/ns)
44: Performance: 6.318 3.799
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (584 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.256 0.128 199.4
44: (ns/day) (hour/ns)
44: Performance: 11.461 2.094
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.231 0.116 199.2
44: (ns/day) (hour/ns)
44: Performance: 6.718 3.573
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.295 0.148 199.5
44: (ns/day) (hour/ns)
44: Performance: 5.257 4.565
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (591 ms)
44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (5143 ms total)
44:
44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.289 0.145 199.3
44: (ns/day) (hour/ns)
44: Performance: 10.133 2.368
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.262 0.132 199.1
44: (ns/day) (hour/ns)
44: Performance: 5.903 4.066
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.343 0.172 199.5
44: (ns/day) (hour/ns)
44: Performance: 4.527 5.301
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (601 ms)
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.325 0.163 199.7
44: (ns/day) (hour/ns)
44: Performance: 9.024 2.660
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.298 0.149 199.6
44: (ns/day) (hour/ns)
44: Performance: 5.209 4.607
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.244 0.122 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.350 3.780
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (584 ms)
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.257 0.129 199.3
44: (ns/day) (hour/ns)
44: Performance: 11.391 2.107
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.269 0.135 199.2
44: (ns/day) (hour/ns)
44: Performance: 5.750 4.174
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.300 0.150 199.4
44: (ns/day) (hour/ns)
44: Performance: 5.174 4.639
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (657 ms)
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.335 0.168 199.4
44: (ns/day) (hour/ns)
44: Performance: 8.736 2.747
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.226 0.113 199.0
44: (ns/day) (hour/ns)
44: Performance: 6.854 3.501
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.238 0.120 199.2
44: (ns/day) (hour/ns)
44: Performance: 6.499 3.693
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (609 ms)
44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (2451 ms total)
44:
44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.183 0.092 199.4
44: (ns/day) (hour/ns)
44: Performance: 15.982 1.502
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.201 0.101 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.723 3.107
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.5
44: (ns/day) (hour/ns)
44: Performance: 7.205 3.331
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (356 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.272 0.136 199.6
44: (ns/day) (hour/ns)
44: Performance: 10.781 2.226
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.184 0.092 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.425 2.849
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.182 0.091 199.4
44: (ns/day) (hour/ns)
44: Performance: 8.529 2.814
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (375 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.288 0.144 199.6
44: (ns/day) (hour/ns)
44: Performance: 10.171 2.360
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.131 3.366
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.249 0.125 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.242 3.845
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (433 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.239 0.120 199.5
44: (ns/day) (hour/ns)
44: Performance: 12.257 1.958
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.234 0.117 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.630 3.620
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.181 0.091 199.4
44: (ns/day) (hour/ns)
44: Performance: 8.545 2.809
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (383 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.274 0.137 199.7
44: (ns/day) (hour/ns)
44: Performance: 10.701 2.243
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.185 0.093 199.6
44: (ns/day) (hour/ns)
44: Performance: 8.367 2.869
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.200 0.100 199.6
44: (ns/day) (hour/ns)
44: Performance: 7.751 3.096
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (384 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.339 0.170 199.7
44: (ns/day) (hour/ns)
44: Performance: 8.655 2.773
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.267 0.134 199.5
44: (ns/day) (hour/ns)
44: Performance: 5.802 4.137
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.231 0.116 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.704 3.580
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (474 ms)
44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (2405 ms total)
44:
44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.223 0.112 199.5
44: (ns/day) (hour/ns)
44: Performance: 13.163 1.823
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.184 0.092 199.2
44: (ns/day) (hour/ns)
44: Performance: 8.422 2.850
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.165 0.083 199.3
44: (ns/day) (hour/ns)
44: Performance: 9.377 2.560
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (343 ms)
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.187 0.094 199.3
44: (ns/day) (hour/ns)
44: Performance: 15.632 1.535
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.130 3.366
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.248 0.124 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.249 3.841
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (383 ms)
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.287 0.144 199.6
44: (ns/day) (hour/ns)
44: Performance: 10.224 2.347
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.234 0.117 199.4
44: (ns/day) (hour/ns)
44: Performance: 6.622 3.624
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.182 0.091 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.533 2.813
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (408 ms)
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.238 0.119 199.6
44: (ns/day) (hour/ns)
44: Performance: 12.295 1.952
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.186 0.093 199.5
44: (ns/day) (hour/ns)
44: Performance: 8.357 2.872
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.167 0.084 199.4
44: (ns/day) (hour/ns)
44: Performance: 9.309 2.578
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (351 ms)
44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (1485 ms total)
44:
44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.269 0.135 199.5
44: (ns/day) (hour/ns)
44: Performance: 10.879 2.206
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.234 0.117 199.4
44: (ns/day) (hour/ns)
44: Performance: 6.636 3.617
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.218 3.325
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (416 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.203 0.102 199.4
44: (ns/day) (hour/ns)
44: Performance: 14.430 1.663
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.167 0.084 199.2
44: (ns/day) (hour/ns)
44: Performance: 9.275 2.587
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.165 0.083 199.3
44: (ns/day) (hour/ns)
44: Performance: 9.409 2.551
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (325 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.220 0.110 199.4
44: (ns/day) (hour/ns)
44: Performance: 13.339 1.799
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.184 0.092 199.2
44: (ns/day) (hour/ns)
44: Performance: 8.433 2.846
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.221 3.324
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (366 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.271 0.136 199.5
44: (ns/day) (hour/ns)
44: Performance: 10.834 2.215
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.147 3.358
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.181 0.091 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.550 2.807
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (392 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Using Berendsen pressure coupling invalidates the true ensemble for the
44: thermostat
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: There was 1 warning
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Using Berendsen pressure coupling invalidates the true ensemble for the
44: thermostat
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: There was 1 warning
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.187 0.094 199.4
44: (ns/day) (hour/ns)
44: Performance: 15.685 1.530
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.150 0.076 199.1
44: (ns/day) (hour/ns)
44: Performance: 10.289 2.332
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.216 3.326
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (333 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.287 0.144 199.6
44: (ns/day) (hour/ns)
44: Performance: 10.202 2.352
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.251 0.126 199.4
44: (ns/day) (hour/ns)
44: Performance: 6.191 3.877
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.165 0.083 199.3
44: (ns/day) (hour/ns)
44: Performance: 9.408 2.551
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (409 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.153 0.077 199.2
44: (ns/day) (hour/ns)
44: Performance: 19.092 1.257
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.134 0.067 199.0
44: (ns/day) (hour/ns)
44: Performance: 11.575 2.073
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.165 0.083 199.2
44: (ns/day) (hour/ns)
44: Performance: 9.411 2.550
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (283 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7
44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (0 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.187 0.094 199.3
44: (ns/day) (hour/ns)
44: Performance: 15.672 1.531
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.200 0.101 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.733 3.103
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.181 0.091 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.561 2.803
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (341 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.173 0.087 199.5
44: (ns/day) (hour/ns)
44: Performance: 16.943 1.417
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.169 0.085 199.5
44: (ns/day) (hour/ns)
44: Performance: 9.188 2.612
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.233 0.117 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.660 3.604
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (343 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10
44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (0 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11
44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (0 ms)
44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact (3208 ms total)
44:
44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact
44: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.257 0.129 199.5
44: (ns/day) (hour/ns)
44: Performance: 11.388 2.107
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.770 0.385 199.8
44: (ns/day) (hour/ns)
44: Performance: 2.018 11.890
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.197 0.099 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.881 3.045
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (674 ms)
44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (674 ms total)
44:
44: [----------] 3 tests from Checking/InitialConstraintsTest
44: [ RUN ] Checking/InitialConstraintsTest.Works/0
44: Setting the LD random seed to -1567192924
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 11.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 1141.954 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc-and-methanol'
44: 1 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.091 0.046 198.6
44: (ns/day) (hour/ns)
44: Performance: 3.756 6.391
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (70 ms)
44: [ RUN ] Checking/InitialConstraintsTest.Works/1
44: Setting the LD random seed to 103288481
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 11.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 1141.954 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc-and-methanol'
44: 1 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.089 0.045 198.9
44: (ns/day) (hour/ns)
44: Performance: 3.875 6.193
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (67 ms)
44: [ RUN ] Checking/InitialConstraintsTest.Works/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
44: Integrator method md-vv-avek is implemented primarily for validation
44: purposes; for molecular dynamics, you should probably be using md or md-vv
44:
44: Setting the LD random seed to 1803886270
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 11.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 1141.954 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc-and-methanol'
44: 1 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.136 0.068 199.0
44: (ns/day) (hour/ns)
44: Performance: 2.528 9.494
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (91 ms)
44: [----------] 3 tests from Checking/InitialConstraintsTest (228 ms total)
44:
44: [----------] Global test environment tear-down
44: [==========] 51 tests from 9 test cases ran. (16738 ms total)
44: [ PASSED ] 51 tests.
44/54 Test #44: MdrunIOTests ........................ Passed 16.77 sec
test 45
Start 45: MdrunTests
45: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunTests.xml"
45: Test timeout computed to be: 600
45: [==========] Running 12 tests from 5 test cases.
45: [----------] Global test environment set-up.
45: [----------] 1 test from DispersionCorrectionTest
45: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]:
45: The Berendsen thermostat does not generate the correct kinetic energy
45: distribution. You might want to consider using the V-rescale thermostat.
45:
45: Setting the LD random seed to -1814522085
45: Generated 2145 of the 2145 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 2145 of the 2145 1-4 parameter combinations
45: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
45: Cleaning up constraints and constant bonded interactions with virtual sites
45: Converted 3 Bonds with virtual sites to connections, 7 left
45: Removed 18 Angles with virtual sites, 21 left
45: Removed 10 Proper Dih.s with virtual sites, 44 left
45: Converted 12 Constraints with virtual sites to connections, 0 left
45: Number of degrees of freedom in T-Coupling group System is 30.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]:
45: There are 9 non-linear virtual site constructions. Their contribution to
45: the energy error is approximated. In most cases this does not affect the
45: error significantly.
45:
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
45: Changing nstlist from 10 to 50, rlist from 1.016 to 1.167
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Alanine dipeptide in vacuo'
45: 200 steps, 0.4 ps.
45: turning H bonds into constraints...
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
45: Calculated rlist for 1x1 atom pair-list as 1.028 nm, buffer size 0.028 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.016 nm, buffer size 0.016 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.305 0.153 199.5
45: (ns/day) (hour/ns)
45: Performance: 227.513 0.105
45: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (235 ms)
45: [----------] 1 test from DispersionCorrectionTest (235 ms total)
45:
45: [----------] 1 test from OriresTest
45: [ RUN ] OriresTest.OriresCanRun
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
45: The Berendsen thermostat does not generate the correct kinetic energy
45: distribution. You might want to consider using the V-rescale thermostat.
45:
45: Setting the LD random seed to 1880792320
45: Generated 2145 of the 2145 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 2145 of the 2145 1-4 parameter combinations
45: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 518.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
45: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank.
45: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164
45:
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1'
45: 10 steps, 0.0 ps.
45: turning H bonds into constraints...
45: turning H bonds into constraints...
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
45: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.205 0.103 199.2
45: (ns/day) (hour/ns)
45: Performance: 18.515 1.296
45: [ OK ] OriresTest.OriresCanRun (775 ms)
45: [----------] 1 test from OriresTest (775 ms total)
45:
45: [----------] 3 tests from PmeTest
45: [ RUN ] PmeTest.ReproducesEnergies
45: Setting the LD random seed to -199781194
45: Generated 8 of the 10 non-bonded parameter combinations
45: Excluding 2 bonded neighbours molecule type 'Methanol'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group rest is 12.00
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
45: NVE simulation: will use the initial temperature of 1046.791 K for
45: determining the Verlet buffer size
45:
45: Estimate for the relative computational load of the PME mesh part: 1.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
45: The optimal PME mesh load for parallel simulations is below 0.5
45: and for highly parallel simulations between 0.25 and 0.33,
45: for higher performance, increase the cut-off and the PME grid spacing.
45:
45:
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 20 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: Calculating fourier grid dimensions for X Y Z
45: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.305 0.153 199.6
45: (ns/day) (hour/ns)
45: Performance: 11.886 2.019
45: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 20 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.204 0.102 199.4
45: (ns/day) (hour/ns)
45: Performance: 17.702 1.356
45: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45:
45: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
45: starting mdrun 'spc-and-methanol'
45: 20 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.204 0.102 199.4
45: (ns/day) (hour/ns)
45: Performance: 17.721 1.354
45: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (10595 ms)
45: [ RUN ] PmeTest.ScalesTheBox
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -1895605848
45: Generated 8 of the 10 non-bonded parameter combinations
45: Excluding 2 bonded neighbours molecule type 'Methanol'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group rest is 12.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
45: NVE simulation: will use the initial temperature of 1046.791 K for
45: determining the Verlet buffer size
45:
45: Estimate for the relative computational load of the PME mesh part: 1.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
45: The optimal PME mesh load for parallel simulations is below 0.5
45: and for highly parallel simulations between 0.25 and 0.33,
45: for higher performance, increase the cut-off and the PME grid spacing.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 0 steps, 0.0 ps.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.004 0.002 176.4
45: (ns/day) (hour/ns)
45: Performance: 36.646 0.655
45: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
45:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: Calculating fourier grid dimensions for X Y Z
45: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
45: This run will generate roughly 0 Mb of data
45: [ OK ] PmeTest.ScalesTheBox (35 ms)
45: [ RUN ] PmeTest.ScalesTheBoxWithWalls
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -1973513501
45: Generated 8 of the 10 non-bonded parameter combinations
45: Excluding 2 bonded neighbours molecule type 'Methanol'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Searching the wall atom type(s)
45: Number of degrees of freedom in T-Coupling group rest is 13.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
45: NVE simulation: will use the initial temperature of 966.268 K for
45: determining the Verlet buffer size
45:
45: Estimate for the relative computational load of the PME mesh part: 1.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
45: The optimal PME mesh load for parallel simulations is below 0.5
45: and for highly parallel simulations between 0.25 and 0.33,
45: for higher performance, increase the cut-off and the PME grid spacing.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 0 steps, 0.0 ps.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.013 0.007 188.8
45: (ns/day) (hour/ns)
45: Performance: 12.226 1.963
45: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
45:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: Calculating fourier grid dimensions for X Y Z
45: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
45: This run will generate roughly 0 Mb of data
45: [ OK ] PmeTest.ScalesTheBoxWithWalls (30624 ms)
45: [----------] 3 tests from PmeTest (41254 ms total)
45:
45: [----------] 1 test from CompelTest
45: [ RUN ] CompelTest.SwapCanRun
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
45: The Berendsen thermostat does not generate the correct kinetic energy
45: distribution. You might want to consider using the V-rescale thermostat.
45:
45: Setting the LD random seed to 1520005331
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 3 bonded neighbours molecule type 'Protein'
45: Excluding 3 bonded neighbours molecule type 'OCT'
45: Excluding 1 bonded neighbours molecule type 'NA'
45: Excluding 1 bonded neighbours molecule type 'CL'
45: Excluding 3 bonded neighbours molecule type 'Protein'
45: Excluding 3 bonded neighbours molecule type 'OCT'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Split0 group 'Ch0' contains 83 atoms.
45: Split1 group 'Ch1' contains 83 atoms.
45: Solvent group 'SOL' contains 11931 atoms.
45: Swap group 'NA+' contains 19 atoms.
45: Swap group 'CL-' contains 19 atoms.
45: Number of degrees of freedom in T-Coupling group System is 27869.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
45: Removing center of mass motion in the presence of position restraints
45: might cause artifacts. When you are using position restraints to
45: equilibrate a macro-molecule, the artifacts are usually negligible.
45:
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: SWAP: Determining initial numbers of ions per compartment.
45: SWAP: Setting pointers for checkpoint writing
45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
45: starting mdrun 'Channel_coco in octane membrane'
45: 2 steps, 0.0 ps.
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
45: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 1 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 2.387 1.194 199.9
45: (ns/day) (hour/ns)
45: Performance: 1.085 22.115
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
45: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: SWAP: Setting pointers for checkpoint writing
45: SWAP: Copying channel fluxes from checkpoint file data
45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
45: starting mdrun 'Channel_coco in octane membrane'
45: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 2.117 1.059 199.9
45: (ns/day) (hour/ns)
45: Performance: 1.224 19.610
45: [ OK ] CompelTest.SwapCanRun (5330 ms)
45: [----------] 1 test from CompelTest (5330 ms total)
45:
45: [----------] 6 tests from BondedInteractionsTest
45: [ RUN ] BondedInteractionsTest.NormalBondWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -1338171379
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 2 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.002 0.001 176.6
45: (ns/day) (hour/ns)
45: Performance: 100.579 0.239
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.NormalBondWorks (21 ms)
45: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 724201468
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 2 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.001 0.001 176.5
45: (ns/day) (hour/ns)
45: Performance: 106.805 0.225
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.TabulatedBondWorks (26 ms)
45: [ RUN ] BondedInteractionsTest.NormalAngleWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -1877130290
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.001 0.001 176.2
45: (ns/day) (hour/ns)
45: Performance: 106.710 0.225
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.NormalAngleWorks (20 ms)
45: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -1040594824
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.001 0.001 175.3
45: (ns/day) (hour/ns)
45: Performance: 107.374 0.224
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (24 ms)
45: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 1612426553
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.001 0.001 176.3
45: (ns/day) (hour/ns)
45: Performance: 106.994 0.224
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.NormalDihedralWorks (21 ms)
45: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -581606976
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.001 0.001 176.2
45: (ns/day) (hour/ns)
45: Performance: 107.247 0.224
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (27 ms)
45: [----------] 6 tests from BondedInteractionsTest (140 ms total)
45:
45: [----------] Global test environment tear-down
45: [==========] 12 tests from 5 test cases ran. (47735 ms total)
45: [ PASSED ] 12 tests.
45:
45: YOU HAVE 12 DISABLED TESTS
45:
45/54 Test #45: MdrunTests .......................... Passed 47.76 sec
test 46
Start 46: MdrunNonIntegratorTests
46: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml"
46: Test timeout computed to be: 600
46: [==========] Running 58 tests from 5 test cases.
46: [----------] Global test environment set-up.
46: [----------] 1 test from NonbondedBenchTest
46: [ RUN ] NonbondedBenchTest.BasicEndToEndTest
46: System size: 3000 atoms
46: Cut-off radius: 1 nm
46: Number of threads: 1
46: Number of iterations: 1
46: Compute energies: no
46: Ewald excl. corr.: analytical
46:
46: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle
46: total useful
46: Ewald all geom. no 0.000 0.0000 inf inf
46: [ OK ] NonbondedBenchTest.BasicEndToEndTest (215 ms)
46: [----------] 1 test from NonbondedBenchTest (215 ms total)
46:
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -4.7990990e+01
46: Maximum force = 1.8629828e+02 on atom 13
46: Norm of force = 8.7721844e+01
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (885 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 3.02331e+02 on atom 3
46: F-Norm = 1.18024e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -5.5862099e+01
46: Maximum force = 4.2728845e+02 on atom 13
46: Norm of force = 1.8453478e+02
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (2362 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.1937714e+02
46: Maximum force = 9.9988643e+03 on atom 9
46: Norm of force = 4.6166996e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (449 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46:
46: NOTE 3 [file glycine_vacuo.top, line 12]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41575e+04 on atom 10
46: F-Norm = 1.18451e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.5174377e+02
46: Maximum force = 7.4208838e+03 on atom 9
46: Norm of force = 3.5693005e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (443 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.5698413e+02
46: Maximum force = 4.5704984e+02 on atom 17
46: Norm of force = 1.8327747e+02
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (70 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46:
46: NOTE 4 [file unknown]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 1.06801e+03 on atom 28
46: F-Norm = 4.26916e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.6941180e+02
46: Maximum force = 2.1832491e+02 on atom 17
46: Norm of force = 7.9220732e+01
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (71 ms)
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (4280 ms total)
46:
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents converged to Fmax < 10 in 1 steps
46: Potential Energy = -9.7425699e-01
46: Maximum force = 4.0132303e+00 on atom 1
46: Norm of force = 1.6383944e+00
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (23 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 4.01323e+00 on atom 1
46: F-Norm = 1.63839e+00
46:
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
46: Potential Energy = -9.9064207e-01
46: Maximum force = 2.5781622e+00 on atom 1
46: Norm of force = 1.0525302e+00
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (23 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46:
46: There was 1 warning
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Low-Memory BFGS Minimizer:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: Using 10 BFGS correction steps.
46:
46: F-max = 4.01323e+00 on atom 1
46: F-Norm = 1.63839e+00
46:
46:
46: writing lowest energy coordinates.
46:
46: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
46: Potential Energy = -9.9064207e-01
46: Maximum force = 2.5781622e+00 on atom 1
46: Norm of force = 1.0525302e+00
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (23 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.1939697e+02
46: Maximum force = 9.9704248e+03 on atom 9
46: Norm of force = 4.6227540e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (444 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41672e+04 on atom 10
46: F-Norm = 1.19357e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.5625757e+02
46: Maximum force = 7.5018242e+03 on atom 9
46: Norm of force = 3.6139019e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (442 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46:
46: There was 1 warning
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Low-Memory BFGS Minimizer:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: Using 10 BFGS correction steps.
46:
46: F-max = 2.41672e+04 on atom 10
46: F-Norm = 1.19357e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 5.6111725e+02
46: Maximum force = 1.2685491e+04 on atom 10
46: Norm of force = 6.0643622e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (443 ms)
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1398 ms total)
46:
46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
46: NVE simulation: will use the initial temperature of 68.810 K for
46: determining the Verlet buffer size
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.242 0.121 199.5
46: (ns/day) (hour/ns)
46: Performance: 12.097 1.984
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr'
46:
46: trr version: GMX_trn_file (single precision)
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.008 0.004 194.3
46: (ns/day) (hour/ns)
46: Performance: 347.134 0.069
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (162 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
46: NVE simulation: will use the initial temperature of 68.810 K for
46: determining the Verlet buffer size
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.204 0.102 199.6
46: (ns/day) (hour/ns)
46: Performance: 14.342 1.673
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.008 0.004 194.3
46: (ns/day) (hour/ns)
46: Performance: 348.785 0.069
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (142 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
46: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.202 0.102 199.5
46: (ns/day) (hour/ns)
46: Performance: 14.469 1.659
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.008 0.004 194.2
46: (ns/day) (hour/ns)
46: Performance: 349.280 0.069
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (141 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.170 0.085 199.4
46: (ns/day) (hour/ns)
46: Performance: 17.271 1.390
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.008 0.004 194.3
46: (ns/day) (hour/ns)
46: Performance: 344.784 0.070
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (125 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: NVE simulation: will use the initial temperature of 398.997 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.217 0.109 199.4
46: (ns/day) (hour/ns)
46: Performance: 13.531 1.774
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.009 0.005 194.6
46: (ns/day) (hour/ns)
46: Performance: 307.860 0.078
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (2490 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: NVE simulation: will use the initial temperature of 398.997 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.208 0.104 199.6
46: (ns/day) (hour/ns)
46: Performance: 14.124 1.699
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.009 0.005 194.4
46: (ns/day) (hour/ns)
46: Performance: 310.717 0.077
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (2481 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.189 0.095 199.4
46: (ns/day) (hour/ns)
46: Performance: 15.473 1.551
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.010 0.005 194.7
46: (ns/day) (hour/ns)
46: Performance: 299.829 0.080
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (2475 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.223 0.112 199.5
46: (ns/day) (hour/ns)
46: Performance: 13.153 1.825
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.009 0.005 194.4
46: (ns/day) (hour/ns)
46: Performance: 304.197 0.079
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (2491 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: NVE simulation: will use the initial temperature of 456.887 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 6 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.193 0.097 199.2
46: (ns/day) (hour/ns)
46: Performance: 15.168 1.582
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.015 0.008 195.1
46: (ns/day) (hour/ns)
46: Performance: 188.825 0.127
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (196 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: NVE simulation: will use the initial temperature of 456.887 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 6 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.223 0.112 199.3
46: (ns/day) (hour/ns)
46: Performance: 13.153 1.825
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.015 0.008 195.5
46: (ns/day) (hour/ns)
46: Performance: 188.403 0.127
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (209 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.220 0.111 199.3
46: (ns/day) (hour/ns)
46: Performance: 13.286 1.806
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.015 0.008 195.4
46: (ns/day) (hour/ns)
46: Performance: 188.501 0.127
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (259 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.204 0.102 199.2
46: (ns/day) (hour/ns)
46: Performance: 14.348 1.673
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.015 0.008 195.4
46: (ns/day) (hour/ns)
46: Performance: 189.271 0.127
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (233 ms)
46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (11405 ms total)
46:
46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.221 0.111 199.1
46: (ns/day) (hour/ns)
46: Performance: 13.227 1.815
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 151.433 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (213 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.229 0.115 199.2
46: (ns/day) (hour/ns)
46: Performance: 12.764 1.880
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.9
46: (ns/day) (hour/ns)
46: Performance: 151.915 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (216 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.229 0.115 199.2
46: (ns/day) (hour/ns)
46: Performance: 12.783 1.877
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.8
46: (ns/day) (hour/ns)
46: Performance: 151.347 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (217 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.263 0.132 199.3
46: (ns/day) (hour/ns)
46: Performance: 11.140 2.154
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.2
46: (ns/day) (hour/ns)
46: Performance: 151.262 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (234 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.227 0.114 199.2
46: (ns/day) (hour/ns)
46: Performance: 12.907 1.859
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.9
46: (ns/day) (hour/ns)
46: Performance: 151.050 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (216 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.211 0.106 199.1
46: (ns/day) (hour/ns)
46: Performance: 13.863 1.731
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 151.076 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (209 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.194 0.097 199.0
46: (ns/day) (hour/ns)
46: Performance: 15.067 1.593
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.8
46: (ns/day) (hour/ns)
46: Performance: 150.832 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (199 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.244 0.122 199.2
46: (ns/day) (hour/ns)
46: Performance: 11.995 2.001
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 151.073 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (225 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.278 0.140 199.2
46: (ns/day) (hour/ns)
46: Performance: 10.522 2.281
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.8
46: (ns/day) (hour/ns)
46: Performance: 152.407 0.157
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (242 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.246 0.123 199.2
46: (ns/day) (hour/ns)
46: Performance: 11.905 2.016
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.8
46: (ns/day) (hour/ns)
46: Performance: 151.344 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (225 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.229 0.115 199.2
46: (ns/day) (hour/ns)
46: Performance: 12.768 1.880
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 151.802 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (216 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.232 0.116 199.5
46: (ns/day) (hour/ns)
46: Performance: 12.633 1.900
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.8
46: (ns/day) (hour/ns)
46: Performance: 152.050 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (218 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.231 0.116 199.5
46: (ns/day) (hour/ns)
46: Performance: 12.670 1.894
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.9
46: (ns/day) (hour/ns)
46: Performance: 151.709 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (216 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.231 0.116 199.5
46: (ns/day) (hour/ns)
46: Performance: 12.700 1.890
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 153.176 0.157
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (217 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.232 0.116 199.5
46: (ns/day) (hour/ns)
46: Performance: 12.657 1.896
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.5
46: (ns/day) (hour/ns)
46: Performance: 152.430 0.157
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (217 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.231 0.116 199.5
46: (ns/day) (hour/ns)
46: Performance: 12.705 1.889
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.1
46: (ns/day) (hour/ns)
46: Performance: 151.556 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (216 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.281 0.141 199.6
46: (ns/day) (hour/ns)
46: Performance: 10.440 2.299
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.2
46: (ns/day) (hour/ns)
46: Performance: 150.899 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (242 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.264 0.132 199.6
46: (ns/day) (hour/ns)
46: Performance: 11.111 2.160
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 151.739 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (233 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.264 0.132 199.6
46: (ns/day) (hour/ns)
46: Performance: 11.112 2.160
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 151.843 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (233 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.247 0.124 199.5
46: (ns/day) (hour/ns)
46: Performance: 11.878 2.020
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 151.814 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (225 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.264 0.132 199.5
46: (ns/day) (hour/ns)
46: Performance: 11.101 2.162
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.9
46: (ns/day) (hour/ns)
46: Performance: 152.452 0.157
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (233 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.232 0.116 199.5
46: (ns/day) (hour/ns)
46: Performance: 12.643 1.898
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.1
46: (ns/day) (hour/ns)
46: Performance: 152.399 0.157
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (216 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.307 0.154 199.4
46: (ns/day) (hour/ns)
46: Performance: 9.533 2.518
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 150.984 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (293 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.238 0.119 199.2
46: (ns/day) (hour/ns)
46: Performance: 12.306 1.950
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 150.273 0.160
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (258 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.320 0.160 199.4
46: (ns/day) (hour/ns)
46: Performance: 9.156 2.621
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.1
46: (ns/day) (hour/ns)
46: Performance: 150.405 0.160
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (300 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.303 0.152 199.4
46: (ns/day) (hour/ns)
46: Performance: 9.651 2.487
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.1
46: (ns/day) (hour/ns)
46: Performance: 151.050 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (291 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.237 0.119 199.2
46: (ns/day) (hour/ns)
46: Performance: 12.347 1.944
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.1
46: (ns/day) (hour/ns)
46: Performance: 150.416 0.160
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (259 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.220 0.110 199.1
46: (ns/day) (hour/ns)
46: Performance: 13.320 1.802
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 150.999 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (250 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.269 0.135 199.2
46: (ns/day) (hour/ns)
46: Performance: 10.861 2.210
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.0
46: (ns/day) (hour/ns)
46: Performance: 150.980 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (275 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.288 0.144 199.3
46: (ns/day) (hour/ns)
46: Performance: 10.181 2.357
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.8
46: (ns/day) (hour/ns)
46: Performance: 149.663 0.160
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (283 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.287 0.144 199.3
46: (ns/day) (hour/ns)
46: Performance: 10.201 2.353
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 194.1
46: (ns/day) (hour/ns)
46: Performance: 151.381 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (283 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.254 0.128 199.3
46: (ns/day) (hour/ns)
46: Performance: 11.516 2.084
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.8
46: (ns/day) (hour/ns)
46: Performance: 150.449 0.160
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (267 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.270 0.136 199.3
46: (ns/day) (hour/ns)
46: Performance: 10.822 2.218
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 193.9
46: (ns/day) (hour/ns)
46: Performance: 150.097 0.160
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (275 ms)
46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (7914 ms total)
46:
46: [----------] Global test environment tear-down
46: [==========] 58 tests from 5 test cases ran. (25212 ms total)
46: [ PASSED ] 58 tests.
46/54 Test #46: MdrunNonIntegratorTests ............. Passed 25.24 sec
test 47
Start 47: MdrunTpiTests
47: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunTpiTests.xml"
47: Test timeout computed to be: 600
47: [==========] Running 2 tests from 1 test case.
47: [----------] Global test environment set-up.
47: [----------] 2 tests from Simple/TpiTest
47: [ RUN ] Simple/TpiTest.ReproducesOutput/0
47: Ignoring obsolete mdp entry 'ns_type'
47: Generated 331705 of the 331705 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 331705 of the 331705 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Excluding 3 bonded neighbours molecule type 'methane'
47: Number of degrees of freedom in T-Coupling group System is 1308.00
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
47: TPI is not implemented for GPUs.
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: Reading frames from gro file '216 water molecules', 648 atoms.
47:
Reading frame 0 time 0.000 mu 8.706e+02 <mu> 8.706e+02
47:
Last frame 0 time 0.000
47: Analysing residue names:
47: There are: 216 Water residues
47: There are: 1 Other residues
47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
47: This run will generate roughly 0 Mb of data
47: [ OK ] Simple/TpiTest.ReproducesOutput/0 (1032 ms)
47: [ RUN ] Simple/TpiTest.ReproducesOutput/1
47: Ignoring obsolete mdp entry 'ns_type'
47: Generated 331705 of the 331705 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 331705 of the 331705 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Excluding 3 bonded neighbours molecule type 'methane'
47: Number of degrees of freedom in T-Coupling group System is 1308.00
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
47: TPI is not implemented for GPUs.
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: Reading frames from gro file '216 water molecules', 648 atoms.
47:
Reading frame 0 time 0.000 mu 9.144e+01 <mu> 9.144e+01
47:
Last frame 0 time 0.000
47: Analysing residue names:
47: There are: 216 Water residues
47: There are: 1 Other residues
47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
47: This run will generate roughly 0 Mb of data
47: [ OK ] Simple/TpiTest.ReproducesOutput/1 (2481 ms)
47: [----------] 2 tests from Simple/TpiTest (3513 ms total)
47:
47: [----------] Global test environment tear-down
47: [==========] 2 tests from 1 test case ran. (3513 ms total)
47: [ PASSED ] 2 tests.
47/54 Test #47: MdrunTpiTests ....................... Passed 3.54 sec
test 48
Start 48: MdrunMpiTests
48: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiTests.xml"
48: Test timeout computed to be: 600
48: [==========] Running 22 tests from 7 test cases.
48: [----------] Global test environment set-up.
48: [----------] 1 test from DomainDecompositionSpecialCasesTest
48: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to 1423771108
48: Generated 3 of the 3 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 3 of the 3 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 9.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 0 steps, 0.0 ps.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.003 0.001 246.1
48: (ns/day) (hour/ns)
48: Performance: 72.930 0.329
48: This run will generate roughly 0 Mb of data
48: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (45 ms)
48: [----------] 1 test from DomainDecompositionSpecialCasesTest (45 ms total)
48:
48: [----------] 4 tests from MimicTest
48: [ RUN ] MimicTest.OneQuantumMol
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to 1648086673
48: Generated 10 of the 10 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 10 of the 10 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 21.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
48:
48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.005 0.001 361.2
48: (ns/day) (hour/ns)
48: Performance: 57.705 0.416
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.OneQuantumMol (26 ms)
48: [ RUN ] MimicTest.AllQuantumMol
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to 668490119
48: Generated 10 of the 10 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 10 of the 10 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 21.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
48:
48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.005 0.001 358.6
48: (ns/day) (hour/ns)
48: Performance: 61.411 0.391
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.AllQuantumMol (25 ms)
48: [ RUN ] MimicTest.TwoQuantumMol
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -349022332
48: Generated 10 of the 10 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 10 of the 10 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 21.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
48:
48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.005 0.001 359.9
48: (ns/day) (hour/ns)
48: Performance: 61.292 0.392
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.TwoQuantumMol (25 ms)
48: [ RUN ] MimicTest.BondCuts
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -302181265
48: Generated 2211 of the 2211 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 2211 of the 2211 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
48: Number of degrees of freedom in T-Coupling group rest is 66.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
48: NVE simulation: will use the initial temperature of 300.368 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
48:
48: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.007 0.002 368.8
48: (ns/day) (hour/ns)
48: Performance: 46.223 0.519
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
48: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.BondCuts (71 ms)
48: [----------] 4 tests from MimicTest (147 ms total)
48:
48: [----------] 1 test from MultiSimTerminationTest
48: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
48: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
48: [----------] 1 test from MultiSimTerminationTest (0 ms total)
48:
48: [----------] 3 tests from PmeTest
48: [ RUN ] PmeTest.ReproducesEnergies
48: Setting the LD random seed to -794347841
48: Generated 8 of the 10 non-bonded parameter combinations
48: Excluding 2 bonded neighbours molecule type 'Methanol'
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 12.00
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
48: NVE simulation: will use the initial temperature of 1046.791 K for
48: determining the Verlet buffer size
48:
48: Estimate for the relative computational load of the PME mesh part: 1.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
48: The optimal PME mesh load for parallel simulations is below 0.5
48: and for highly parallel simulations between 0.25 and 0.33,
48: for higher performance, increase the cut-off and the PME grid spacing.
48:
48:
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 20 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: Calculating fourier grid dimensions for X Y Z
48: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.582 0.146 399.0
48: (ns/day) (hour/ns)
48: Performance: 12.432 1.930
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 20 steps, 0.0 ps.
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.400 0.100 398.6
48: (ns/day) (hour/ns)
48: Performance: 18.060 1.329
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
48: starting mdrun 'spc-and-methanol'
48: 20 steps, 0.0 ps.
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.501 0.126 398.9
48: (ns/day) (hour/ns)
48: Performance: 14.432 1.663
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (10589 ms)
48: [ RUN ] PmeTest.ScalesTheBox
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to 427966566
48: Generated 8 of the 10 non-bonded parameter combinations
48: Excluding 2 bonded neighbours molecule type 'Methanol'
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 12.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
48: NVE simulation: will use the initial temperature of 1046.791 K for
48: determining the Verlet buffer size
48:
48: Estimate for the relative computational load of the PME mesh part: 1.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
48: The optimal PME mesh load for parallel simulations is below 0.5
48: and for highly parallel simulations between 0.25 and 0.33,
48: for higher performance, increase the cut-off and the PME grid spacing.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 0 steps, 0.0 ps.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.008 0.002 339.9
48: (ns/day) (hour/ns)
48: Performance: 36.075 0.665
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: Calculating fourier grid dimensions for X Y Z
48: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
48: This run will generate roughly 0 Mb of data
48: [ OK ] PmeTest.ScalesTheBox (37 ms)
48: [ RUN ] PmeTest.ScalesTheBoxWithWalls
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to 376884276
48: Generated 8 of the 10 non-bonded parameter combinations
48: Excluding 2 bonded neighbours molecule type 'Methanol'
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Searching the wall atom type(s)
48: Number of degrees of freedom in T-Coupling group rest is 13.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
48: NVE simulation: will use the initial temperature of 966.268 K for
48: determining the Verlet buffer size
48:
48: Estimate for the relative computational load of the PME mesh part: 1.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
48: The optimal PME mesh load for parallel simulations is below 0.5
48: and for highly parallel simulations between 0.25 and 0.33,
48: for higher performance, increase the cut-off and the PME grid spacing.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 0 steps, 0.0 ps.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.027 0.007 372.7
48: (ns/day) (hour/ns)
48: Performance: 12.053 1.991
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: Calculating fourier grid dimensions for X Y Z
48: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
48: This run will generate roughly 0 Mb of data
48: [ OK ] PmeTest.ScalesTheBoxWithWalls (30611 ms)
48: [----------] 3 tests from PmeTest (41237 ms total)
48:
48: [----------] 1 test from ReplicaExchangeTerminationTest
48: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
48: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
48: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total)
48:
48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -4.7991020e+01
48: Maximum force = 1.8629866e+02 on atom 13
48: Norm of force = 8.7722033e+01
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (2328 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 3.02331e+02 on atom 3
48: F-Norm = 1.18024e+02
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -5.5862247e+01
48: Maximum force = 4.2727914e+02 on atom 13
48: Norm of force = 1.8453180e+02
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (2331 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 22.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 3.1937704e+02
48: Maximum force = 9.9988633e+03 on atom 9
48: Norm of force = 4.6166993e+03
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (446 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48:
48: NOTE 3 [file glycine_vacuo.top, line 12]:
48: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
48:
48: Number of degrees of freedom in T-Coupling group System is 22.00
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 2.41575e+04 on atom 10
48: F-Norm = 1.18451e+04
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 1.5174442e+02
48: Maximum force = 7.4208892e+03 on atom 9
48: Norm of force = 3.5693002e+03
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (447 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 2145 of the 2145 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 2145 of the 2145 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
48:
48: NOTE 3 [file unknown]:
48: You are using constraints on all bonds, whereas the forcefield has been
48: parametrized only with constraints involving hydrogen atoms. We suggest
48: using constraints = h-bonds instead, this will also improve performance.
48:
48: Cleaning up constraints and constant bonded interactions with virtual sites
48: Removed 18 Angles with virtual sites, 21 left
48: Removed 10 Proper Dih.s with virtual sites, 44 left
48: Converted 15 Constraints with virtual sites to connections, 7 left
48: Number of degrees of freedom in T-Coupling group System is 23.00
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -1.5698419e+02
48: Maximum force = 4.5704996e+02 on atom 17
48: Norm of force = 1.8327748e+02
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (74 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 2145 of the 2145 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 2145 of the 2145 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
48:
48: NOTE 3 [file unknown]:
48: You are using constraints on all bonds, whereas the forcefield has been
48: parametrized only with constraints involving hydrogen atoms. We suggest
48: using constraints = h-bonds instead, this will also improve performance.
48:
48:
48: NOTE 4 [file unknown]:
48: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
48:
48: Cleaning up constraints and constant bonded interactions with virtual sites
48: Removed 18 Angles with virtual sites, 21 left
48: Removed 10 Proper Dih.s with virtual sites, 44 left
48: Converted 15 Constraints with virtual sites to connections, 7 left
48: Number of degrees of freedom in T-Coupling group System is 23.00
48:
48: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 5 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 1.06801e+03 on atom 28
48: F-Norm = 4.26916e+02
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -1.6941193e+02
48: Maximum force = 2.1835349e+02 on atom 17
48: Norm of force = 7.9216550e+01
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (77 ms)
48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (5704 ms total)
48:
48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents converged to Fmax < 10 in 1 steps
48: Potential Energy = -9.7425699e-01
48: Maximum force = 4.0132303e+00 on atom 3
48: Norm of force = 1.6383944e+00
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (25 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 4.01323e+00 on atom 3
48: F-Norm = 1.63839e+00
48:
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
48: Potential Energy = -9.9064207e-01
48: Maximum force = 2.5781622e+00 on atom 3
48: Norm of force = 1.0525302e+00
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (27 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48:
48: There was 1 warning
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (12 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 3.1939685e+02
48: Maximum force = 9.9704248e+03 on atom 9
48: Norm of force = 4.6227568e+03
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (446 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 2.41672e+04 on atom 10
48: F-Norm = 1.19357e+04
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 1.5625764e+02
48: Maximum force = 7.5018237e+03 on atom 9
48: Norm of force = 3.6139019e+03
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (450 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48:
48: There was 1 warning
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (427 ms)
48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1387 ms total)
48:
48: [----------] Global test environment tear-down
48: [==========] 22 tests from 7 test cases ran. (48520 ms total)
48: [ PASSED ] 22 tests.
48:
48: YOU HAVE 4 DISABLED TESTS
48:
48/54 Test #48: MdrunMpiTests ....................... Passed 48.55 sec
test 49
Start 49: MdrunMpiCoordinationTestsOneRank
49: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml"
49: Test timeout computed to be: 480
49: [==========] Running 27 tests from 3 test cases.
49: [----------] Global test environment set-up.
49: [----------] 1 test from BasicPropagators/PeriodicActionsTest
49: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.118 0.119 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.387 1.937
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.104 0.105 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.023 1.711
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.076 0.076 99.6
49: (ns/day) (hour/ns)
49: Performance: 19.348 1.240
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.564 1.648
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.078 0.078 99.6
49: (ns/day) (hour/ns)
49: Performance: 18.769 1.279
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.111 0.112 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.148 1.825
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (746 ms)
49: [----------] 1 test from BasicPropagators/PeriodicActionsTest (746 ms total)
49:
49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.502 1.655
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.097 0.097 99.7
49: (ns/day) (hour/ns)
49: Performance: 15.167 1.582
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.093 0.093 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.796 1.519
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.508 1.654
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.103 0.103 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.237 1.686
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.103 0.103 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.232 1.686
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (733 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.102 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.444 1.662
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.088 0.089 99.6
49: (ns/day) (hour/ns)
49: Performance: 16.552 1.450
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.092 0.092 99.5
49: (ns/day) (hour/ns)
49: Performance: 15.948 1.505
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.108 0.109 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.502 1.778
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.103 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.280 1.681
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.111 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.270 1.809
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (742 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.092 0.093 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.822 1.517
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.088 0.088 99.6
49: (ns/day) (hour/ns)
49: Performance: 16.604 1.445
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.091 0.092 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.996 1.500
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.691 1.634
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.085 0.086 99.6
49: (ns/day) (hour/ns)
49: Performance: 17.161 1.399
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.094 0.094 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.598 1.539
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (692 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.092 0.093 99.7
49: (ns/day) (hour/ns)
49: Performance: 15.842 1.515
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.097 0.097 99.7
49: (ns/day) (hour/ns)
49: Performance: 15.159 1.583
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.084 0.084 99.6
49: (ns/day) (hour/ns)
49: Performance: 17.415 1.378
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.084 0.084 99.6
49: (ns/day) (hour/ns)
49: Performance: 17.461 1.374
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.078 0.078 99.6
49: (ns/day) (hour/ns)
49: Performance: 18.791 1.277
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.103 0.103 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.194 1.691
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (674 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.109 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.417 1.789
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.096 0.097 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.163 1.583
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.092 0.092 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.984 1.502
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.092 0.092 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.963 1.503
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.103 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.328 1.675
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.103 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.329 1.675
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (734 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.517 1.653
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.088 0.089 99.6
49: (ns/day) (hour/ns)
49: Performance: 16.594 1.446
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.108 0.108 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.586 1.766
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.697 1.633
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.094 0.094 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.613 1.537
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.077 0.077 99.5
49: (ns/day) (hour/ns)
49: Performance: 18.971 1.265
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (708 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.093 0.093 99.7
49: (ns/day) (hour/ns)
49: Performance: 15.819 1.517
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.122 0.122 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.025 1.996
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.084 0.084 99.6
49: (ns/day) (hour/ns)
49: Performance: 17.449 1.375
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.083 0.084 99.6
49: (ns/day) (hour/ns)
49: Performance: 17.547 1.368
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.103 0.103 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.279 1.681
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.103 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.291 1.679
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (724 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.376 1.794
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.096 0.096 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.224 1.577
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.091 0.092 99.6
49: (ns/day) (hour/ns)
49: Performance: 16.003 1.500
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.083 0.084 99.5
49: (ns/day) (hour/ns)
49: Performance: 17.546 1.368
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.094 0.094 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.593 1.539
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.103 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.297 1.679
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (717 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.092 0.093 99.7
49: (ns/day) (hour/ns)
49: Performance: 15.833 1.516
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.097 0.097 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.161 1.583
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.685 1.634
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.670 1.636
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.102 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.339 1.674
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.111 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.254 1.811
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (742 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.538 1.651
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.105 0.105 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.929 1.723
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.109 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.427 1.788
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.543 1.650
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.086 0.087 99.6
49: (ns/day) (hour/ns)
49: Performance: 16.964 1.415
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.095 0.095 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.457 1.553
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (733 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.340 1.799
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.163 0.164 99.8
49: (ns/day) (hour/ns)
49: Performance: 8.976 2.674
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.109 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.484 1.780
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.627 1.641
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.086 0.086 99.6
49: (ns/day) (hour/ns)
49: Performance: 17.057 1.407
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.094 0.094 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.574 1.541
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (800 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.084 0.084 99.6
49: (ns/day) (hour/ns)
49: Performance: 17.382 1.381
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.105 0.105 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.957 1.720
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.116 0.117 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.570 1.909
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.091 0.092 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.998 1.500
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.085 0.086 99.6
49: (ns/day) (hour/ns)
49: Performance: 17.111 1.403
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.103 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.320 1.676
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (725 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.102 99.8
49: (ns/day) (hour/ns)
49: Performance: 14.383 1.669
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.106 0.106 99.8
49: (ns/day) (hour/ns)
49: Performance: 13.863 1.731
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.077 0.077 99.7
49: (ns/day) (hour/ns)
49: Performance: 19.082 1.258
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.093 0.094 99.8
49: (ns/day) (hour/ns)
49: Performance: 15.705 1.528
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.104 0.104 99.8
49: (ns/day) (hour/ns)
49: Performance: 14.102 1.702
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.112 0.112 99.8
49: (ns/day) (hour/ns)
49: Performance: 13.080 1.835
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (724 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.369 1.795
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.080 0.080 99.6
49: (ns/day) (hour/ns)
49: Performance: 18.266 1.314
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.092 0.092 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.936 1.506
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.075 0.076 99.5
49: (ns/day) (hour/ns)
49: Performance: 19.449 1.234
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.119 0.120 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.286 1.953
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.111 0.111 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.208 1.817
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (725 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.102 99.8
49: (ns/day) (hour/ns)
49: Performance: 14.400 1.667
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.098 0.098 99.8
49: (ns/day) (hour/ns)
49: Performance: 15.019 1.598
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.085 0.085 99.8
49: (ns/day) (hour/ns)
49: Performance: 17.274 1.389
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.102 99.8
49: (ns/day) (hour/ns)
49: Performance: 14.468 1.659
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.095 0.096 99.8
49: (ns/day) (hour/ns)
49: Performance: 15.375 1.561
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.095 0.096 99.8
49: (ns/day) (hour/ns)
49: Performance: 15.367 1.562
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (708 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.159 0.159 99.8
49: (ns/day) (hour/ns)
49: Performance: 9.215 2.605
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.105 0.105 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.976 1.717
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.092 0.092 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.948 1.505
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.639 1.639
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.103 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.294 1.679
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.094 0.094 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.568 1.542
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (791 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.076 0.076 99.6
49: (ns/day) (hour/ns)
49: Performance: 19.212 1.249
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.097 0.097 99.7
49: (ns/day) (hour/ns)
49: Performance: 15.138 1.585
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.093 0.093 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.800 1.519
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.093 0.093 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.789 1.520
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.078 0.078 99.5
49: (ns/day) (hour/ns)
49: Performance: 18.777 1.278
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.078 0.078 99.5
49: (ns/day) (hour/ns)
49: Performance: 18.749 1.280
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (650 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.076 0.077 99.5
49: (ns/day) (hour/ns)
49: Performance: 19.120 1.255
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.072 0.072 99.5
49: (ns/day) (hour/ns)
49: Performance: 20.399 1.177
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.092 0.092 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.978 1.502
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.091 0.092 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.996 1.500
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.094 0.094 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.593 1.539
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.094 0.094 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.593 1.539
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (659 ms)
49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (12982 ms total)
49:
49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.132 0.132 99.8
49: (ns/day) (hour/ns)
49: Performance: 11.137 2.155
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.086 0.087 99.6
49: (ns/day) (hour/ns)
49: Performance: 16.930 1.418
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.374 1.794
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.111 0.112 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.140 1.826
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.112 0.112 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.075 1.836
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.142 0.142 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.336 2.322
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (14823 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.128 0.128 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.435 2.099
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.087 0.087 99.6
49: (ns/day) (hour/ns)
49: Performance: 16.896 1.420
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.118 0.118 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.426 1.931
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.129 0.130 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.334 2.118
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.108 0.108 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.577 1.768
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.125 0.125 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.752 2.042
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (14790 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.102 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.421 1.664
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.516 1.653
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.106 0.107 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.790 1.740
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.124 0.124 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.840 2.027
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.120 0.120 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.252 1.959
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.114 0.114 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.877 1.864
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (14756 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.104 0.104 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.094 1.703
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.114 0.114 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.834 1.870
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.112 0.112 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.065 1.837
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.115 0.115 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.782 1.878
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.131 0.131 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.211 2.141
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.104 0.104 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.131 1.698
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (14765 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.106 0.106 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.857 1.732
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.118 0.118 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.447 1.928
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.121 0.121 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.104 1.983
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.108 0.109 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.503 1.777
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.117 0.117 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.526 1.916
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.104 0.104 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.091 1.703
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (14764 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.101 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.583 1.646
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.119 0.120 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.269 1.956
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.120 0.121 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.167 1.973
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.144 0.145 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.150 2.365
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.121 0.122 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.058 1.990
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.119 0.120 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.267 1.957
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (14823 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.120 0.120 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.246 1.960
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.111 99.8
49: (ns/day) (hour/ns)
49: Performance: 13.287 1.806
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.102 99.8
49: (ns/day) (hour/ns)
49: Performance: 14.407 1.666
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.091 0.091 99.8
49: (ns/day) (hour/ns)
49: Performance: 16.065 1.494
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.114 0.115 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.804 1.874
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.121 0.121 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.124 1.980
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (14739 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.508 1.654
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.112 0.112 99.8
49: (ns/day) (hour/ns)
49: Performance: 13.135 1.827
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.096 0.096 99.7
49: (ns/day) (hour/ns)
49: Performance: 15.238 1.575
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.098 0.098 99.8
49: (ns/day) (hour/ns)
49: Performance: 14.995 1.601
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.120 0.120 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.196 1.968
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.120 0.121 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.177 1.971
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (14748 ms)
49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (118208 ms total)
49:
49: [----------] Global test environment tear-down
49: [==========] 27 tests from 3 test cases ran. (131936 ms total)
49: [ PASSED ] 27 tests.
49/54 Test #49: MdrunMpiCoordinationTestsOneRank .... Passed 131.97 sec
test 50
Start 50: MdrunMpiCoordinationTestsTwoRanks
50: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsTwoRanks.xml"
50: Test timeout computed to be: 480
50: [==========] Running 27 tests from 3 test cases.
50: [----------] Global test environment set-up.
50: [----------] 1 test from BasicPropagators/PeriodicActionsTest
50: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.242 0.121 199.3
50: (ns/day) (hour/ns)
50: Performance: 12.093 1.985
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.253 0.127 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.558 2.076
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.212 0.107 199.1
50: (ns/day) (hour/ns)
50: Performance: 13.781 1.742
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.197 0.099 199.0
50: (ns/day) (hour/ns)
50: Performance: 14.811 1.620
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.168 0.084 198.8
50: (ns/day) (hour/ns)
50: Performance: 17.415 1.378
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.151 0.076 198.6
50: (ns/day) (hour/ns)
50: Performance: 19.284 1.245
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (784 ms)
50: [----------] 1 test from BasicPropagators/PeriodicActionsTest (784 ms total)
50:
50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.149 0.075 198.8
50: (ns/day) (hour/ns)
50: Performance: 19.585 1.225
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.171 0.086 198.9
50: (ns/day) (hour/ns)
50: Performance: 17.077 1.405
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.163 0.082 198.8
50: (ns/day) (hour/ns)
50: Performance: 17.866 1.343
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.180 0.091 198.8
50: (ns/day) (hour/ns)
50: Performance: 16.208 1.481
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.184 0.093 198.9
50: (ns/day) (hour/ns)
50: Performance: 15.838 1.515
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.201 0.101 199.0
50: (ns/day) (hour/ns)
50: Performance: 14.553 1.649
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (675 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.216 0.108 199.1
50: (ns/day) (hour/ns)
50: Performance: 13.546 1.772
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.254 0.128 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.498 2.087
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.212 0.106 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.793 1.740
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.212 0.106 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.804 1.739
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.166 0.084 198.6
50: (ns/day) (hour/ns)
50: Performance: 17.535 1.369
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.149 0.075 198.5
50: (ns/day) (hour/ns)
50: Performance: 19.514 1.230
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (759 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.182 0.091 198.9
50: (ns/day) (hour/ns)
50: Performance: 16.075 1.493
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.187 0.094 198.8
50: (ns/day) (hour/ns)
50: Performance: 15.600 1.538
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.194 0.098 198.7
50: (ns/day) (hour/ns)
50: Performance: 15.018 1.598
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.194 0.098 198.7
50: (ns/day) (hour/ns)
50: Performance: 15.014 1.599
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.183 0.092 198.6
50: (ns/day) (hour/ns)
50: Performance: 15.982 1.502
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.149 0.075 198.3
50: (ns/day) (hour/ns)
50: Performance: 19.557 1.227
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (700 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.148 0.074 198.7
50: (ns/day) (hour/ns)
50: Performance: 19.765 1.214
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.187 0.094 198.9
50: (ns/day) (hour/ns)
50: Performance: 15.597 1.539
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.246 0.123 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.910 2.015
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.263 0.132 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.122 2.158
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.200 0.101 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.585 1.645
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.200 0.101 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.612 1.643
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (774 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.199 0.100 199.0
50: (ns/day) (hour/ns)
50: Performance: 14.722 1.630
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.171 0.086 198.6
50: (ns/day) (hour/ns)
50: Performance: 17.107 1.403
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.244 0.123 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.962 2.006
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.228 0.115 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.827 1.871
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.216 0.109 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.526 1.774
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.183 0.092 198.7
50: (ns/day) (hour/ns)
50: Performance: 15.982 1.502
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (776 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.197 0.099 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.806 1.621
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.187 0.094 198.8
50: (ns/day) (hour/ns)
50: Performance: 15.620 1.536
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.228 0.114 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.841 1.869
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.261 0.131 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.221 2.139
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.265 0.133 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.019 2.178
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.265 0.133 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.032 2.176
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (858 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.265 0.133 199.3
50: (ns/day) (hour/ns)
50: Performance: 11.067 2.169
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.204 0.103 199.0
50: (ns/day) (hour/ns)
50: Performance: 14.306 1.678
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.213 0.107 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.695 1.752
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.230 0.115 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.722 1.886
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.234 0.117 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.502 1.920
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.267 0.134 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.974 2.187
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (857 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.282 0.142 199.3
50: (ns/day) (hour/ns)
50: Performance: 10.377 2.313
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.221 0.111 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.253 1.811
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.162 0.081 198.6
50: (ns/day) (hour/ns)
50: Performance: 18.036 1.331
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.357 0.179 199.3
50: (ns/day) (hour/ns)
50: Performance: 8.211 2.923
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.237 0.119 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.308 1.950
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.216 0.109 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.527 1.774
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (892 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.181 0.091 198.9
50: (ns/day) (hour/ns)
50: Performance: 16.143 1.487
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.187 0.094 198.8
50: (ns/day) (hour/ns)
50: Performance: 15.631 1.535
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.128 0.065 198.2
50: (ns/day) (hour/ns)
50: Performance: 22.772 1.054
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.178 0.089 198.7
50: (ns/day) (hour/ns)
50: Performance: 16.431 1.461
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.216 0.109 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.532 1.774
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.182 0.092 198.7
50: (ns/day) (hour/ns)
50: Performance: 15.998 1.500
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (691 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.198 0.099 199.1
50: (ns/day) (hour/ns)
50: Performance: 14.781 1.624
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.205 0.103 199.0
50: (ns/day) (hour/ns)
50: Performance: 14.293 1.679
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.164 0.082 198.8
50: (ns/day) (hour/ns)
50: Performance: 17.843 1.345
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.180 0.091 198.8
50: (ns/day) (hour/ns)
50: Performance: 16.219 1.480
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.184 0.093 198.9
50: (ns/day) (hour/ns)
50: Performance: 15.870 1.512
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.217 0.109 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.468 1.782
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (724 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.215 0.108 199.1
50: (ns/day) (hour/ns)
50: Performance: 13.575 1.768
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.220 0.111 199.1
50: (ns/day) (hour/ns)
50: Performance: 13.277 1.808
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.179 0.090 198.6
50: (ns/day) (hour/ns)
50: Performance: 16.335 1.469
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.145 0.073 198.3
50: (ns/day) (hour/ns)
50: Performance: 20.083 1.195
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.167 0.084 198.5
50: (ns/day) (hour/ns)
50: Performance: 17.501 1.371
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.182 0.091 198.7
50: (ns/day) (hour/ns)
50: Performance: 16.065 1.494
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (709 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.231 0.116 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.666 1.895
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.187 0.094 198.8
50: (ns/day) (hour/ns)
50: Performance: 15.611 1.537
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.194 0.098 198.8
50: (ns/day) (hour/ns)
50: Performance: 15.014 1.598
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.211 0.106 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.835 1.735
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.198 0.100 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.735 1.629
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.165 0.083 198.6
50: (ns/day) (hour/ns)
50: Performance: 17.643 1.360
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (750 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.150 0.075 198.6
50: (ns/day) (hour/ns)
50: Performance: 19.457 1.233
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.190 0.095 198.9
50: (ns/day) (hour/ns)
50: Performance: 15.383 1.560
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.199 0.100 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.697 1.633
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.199 0.100 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.707 1.632
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.203 0.102 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.375 1.670
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.220 0.110 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.299 1.805
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (725 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.198 0.099 199.0
50: (ns/day) (hour/ns)
50: Performance: 14.773 1.625
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.171 0.086 198.7
50: (ns/day) (hour/ns)
50: Performance: 17.114 1.402
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.178 0.090 198.7
50: (ns/day) (hour/ns)
50: Performance: 16.381 1.465
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.179 0.090 198.7
50: (ns/day) (hour/ns)
50: Performance: 16.351 1.468
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.183 0.092 198.7
50: (ns/day) (hour/ns)
50: Performance: 15.952 1.505
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.200 0.100 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.624 1.641
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (708 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.184 0.093 198.9
50: (ns/day) (hour/ns)
50: Performance: 15.868 1.512
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.156 0.079 198.6
50: (ns/day) (hour/ns)
50: Performance: 18.646 1.287
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.149 0.075 198.5
50: (ns/day) (hour/ns)
50: Performance: 19.581 1.226
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.165 0.083 198.6
50: (ns/day) (hour/ns)
50: Performance: 17.666 1.359
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.203 0.102 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.388 1.668
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.203 0.102 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.385 1.668
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (675 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.197 0.099 199.0
50: (ns/day) (hour/ns)
50: Performance: 14.814 1.620
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.154 0.077 198.6
50: (ns/day) (hour/ns)
50: Performance: 18.977 1.265
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.161 0.081 198.6
50: (ns/day) (hour/ns)
50: Performance: 18.082 1.327
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.145 0.073 198.4
50: (ns/day) (hour/ns)
50: Performance: 20.151 1.191
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.166 0.083 198.6
50: (ns/day) (hour/ns)
50: Performance: 17.627 1.362
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.199 0.100 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.673 1.636
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (667 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.181 0.091 199.0
50: (ns/day) (hour/ns)
50: Performance: 16.102 1.491
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.204 0.103 199.0
50: (ns/day) (hour/ns)
50: Performance: 14.321 1.676
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.180 0.090 198.8
50: (ns/day) (hour/ns)
50: Performance: 16.237 1.478
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.180 0.091 198.8
50: (ns/day) (hour/ns)
50: Performance: 16.214 1.480
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.167 0.084 198.7
50: (ns/day) (hour/ns)
50: Performance: 17.478 1.373
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.167 0.084 198.8
50: (ns/day) (hour/ns)
50: Performance: 17.471 1.374
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (691 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.199 0.100 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.717 1.631
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.220 0.111 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.256 1.810
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.194 0.098 198.8
50: (ns/day) (hour/ns)
50: Performance: 15.023 1.598
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.178 0.089 198.7
50: (ns/day) (hour/ns)
50: Performance: 16.434 1.460
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.182 0.092 198.7
50: (ns/day) (hour/ns)
50: Performance: 16.019 1.498
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.149 0.075 198.4
50: (ns/day) (hour/ns)
50: Performance: 19.575 1.226
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (717 ms)
50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (13349 ms total)
50:
50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.268 0.135 199.3
50: (ns/day) (hour/ns)
50: Performance: 10.919 2.198
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.230 0.115 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.723 1.886
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.219 0.110 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.357 1.797
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.345 0.173 199.3
50: (ns/day) (hour/ns)
50: Performance: 8.485 2.829
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.259 0.130 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.304 2.123
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.240 0.121 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.189 1.969
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (14807 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.231 0.116 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.678 1.893
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.274 0.137 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.694 2.244
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.191 0.096 198.7
50: (ns/day) (hour/ns)
50: Performance: 15.291 1.570
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.271 0.136 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.793 2.224
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.288 0.145 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.143 2.366
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.269 0.135 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.863 2.209
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (14757 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.205 0.103 199.0
50: (ns/day) (hour/ns)
50: Performance: 14.226 1.687
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.191 0.096 198.9
50: (ns/day) (hour/ns)
50: Performance: 15.304 1.568
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.223 0.112 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.125 1.829
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.220 0.111 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.273 1.808
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.191 0.096 198.8
50: (ns/day) (hour/ns)
50: Performance: 15.267 1.572
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.311 0.156 199.3
50: (ns/day) (hour/ns)
50: Performance: 9.408 2.551
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (14681 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.223 0.112 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.090 1.833
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.239 0.120 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.207 1.966
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.212 0.107 198.8
50: (ns/day) (hour/ns)
50: Performance: 13.753 1.745
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.225 0.113 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.010 1.845
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.248 0.125 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.794 2.035
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.226 0.114 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.898 1.861
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (14707 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.269 0.135 199.3
50: (ns/day) (hour/ns)
50: Performance: 10.879 2.206
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.201 0.101 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.550 1.650
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.228 0.114 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.834 1.870
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.205 0.103 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.234 1.686
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.245 0.123 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.951 2.008
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.190 0.095 198.8
50: (ns/day) (hour/ns)
50: Performance: 15.401 1.558
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (14680 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.246 0.123 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.895 2.018
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.262 0.132 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.144 2.154
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.253 0.127 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.577 2.073
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.255 0.128 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.479 2.091
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.229 0.115 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.750 1.882
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.231 0.116 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.660 1.896
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (14757 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.218 0.109 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.431 1.787
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.211 0.106 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.865 1.731
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.223 0.112 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.098 1.832
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.252 0.127 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.581 2.072
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.214 0.107 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.685 1.754
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.237 0.119 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.352 1.943
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (14697 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.250 0.126 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.674 2.056
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.530 0.265 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.534 4.337
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.262 0.131 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.172 2.148
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.245 0.123 198.9
50: (ns/day) (hour/ns)
50: Performance: 11.920 2.013
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.259 0.130 198.8
50: (ns/day) (hour/ns)
50: Performance: 11.256 2.132
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.237 0.119 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.323 1.948
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (14906 ms)
50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (117993 ms total)
50:
50: [----------] Global test environment tear-down
50: [==========] 27 tests from 3 test cases ran. (132127 ms total)
50: [ PASSED ] 27 tests.
50/54 Test #50: MdrunMpiCoordinationTestsTwoRanks ... Passed 132.16 sec
test 51
Start 51: GmxapiExternalInterfaceTests
51: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiExternalInterfaceTests.xml"
51: Test timeout computed to be: 600
51: [==========] Running 9 tests from 2 test cases.
51: [----------] Global test environment set-up.
51: [----------] 8 tests from GmxApiTest
51: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
51: Setting the LD random seed to -1879930363
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 2 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.224 0.112 199.4
51: (ns/day) (hour/ns)
51: Performance: 4.502 5.331
51: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (1022 ms)
51: [ RUN ] GmxApiTest.SystemConstruction
51: Setting the LD random seed to -466456513
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51: [ OK ] GmxApiTest.SystemConstruction (2352 ms)
51: [ RUN ] GmxApiTest.SaneVersionComparisons
51: [ OK ] GmxApiTest.SaneVersionComparisons (1 ms)
51: [ RUN ] GmxApiTest.VersionNamed0_1_Features
51: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms)
51: [ RUN ] GmxApiTest.RunnerBasicMD
51: Setting the LD random seed to 204288578
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 2 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.186 0.094 197.8
51: (ns/day) (hour/ns)
51: Performance: 5.375 4.465
51: [ OK ] GmxApiTest.RunnerBasicMD (2456 ms)
51: [ RUN ] GmxApiTest.RunnerReinitialize
51: Setting the LD random seed to -545192567
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 20 steps, 0.0 ps.
51:
51:
51: Received the remote INT/TERM signal, stopping within 50 steps
51:
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.256 0.129 199.4
51: (ns/day) (hour/ns)
51: Performance: 27.556 0.871
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 20 steps, 0.0 ps.
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.243 0.122 199.2
51: (ns/day) (hour/ns)
51: Performance: 29.107 0.825
51: [ OK ] GmxApiTest.RunnerReinitialize (2624 ms)
51: [ RUN ] GmxApiTest.RunnerContinuedMD
51: Setting the LD random seed to -630056942
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 10 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.292 0.146 199.5
51: (ns/day) (hour/ns)
51: Performance: 12.680 1.893
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
51: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 20 steps, 0.0 ps.
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.259 0.130 199.3
51: (ns/day) (hour/ns)
51: Performance: 27.293 0.879
51: [ OK ] GmxApiTest.RunnerContinuedMD (2658 ms)
51: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
51: Setting the LD random seed to -1872279202
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
51: Changing nstlist from 10 to 1, rlist from 1.041 to 1
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 1 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.223 0.112 199.4
51: (ns/day) (hour/ns)
51: Performance: 3.016 7.956
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
51: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
51: Changing nstlist from 10 to 1, rlist from 1.041 to 1
51:
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 2 steps, 0.0 ps.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.259 0.130 199.4
51: (ns/day) (hour/ns)
51: Performance: 2.595 9.250
51: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (2615 ms)
51: [----------] 8 tests from GmxApiTest (13728 ms total)
51:
51: [----------] 1 test from GmxApiBasicTest
51: [ RUN ] GmxApiBasicTest.Status
51: [ OK ] GmxApiBasicTest.Status (0 ms)
51: [----------] 1 test from GmxApiBasicTest (0 ms total)
51:
51: [----------] Global test environment tear-down
51: [==========] 9 tests from 2 test cases ran. (13729 ms total)
51: [ PASSED ] 9 tests.
51/54 Test #51: GmxapiExternalInterfaceTests ........ Passed 13.75 sec
test 52
Start 52: GmxapiMpiTests
52: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxapi-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiMpiTests.xml"
52: Test timeout computed to be: 600
52: [==========] Running 9 tests from 2 test cases.
52: [----------] Global test environment set-up.
52: [----------] 8 tests from GmxApiTest
52: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
52: Setting the LD random seed to -695327126
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 2 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.233 0.117 199.4
52: (ns/day) (hour/ns)
52: Performance: 4.339 5.531
52: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (999 ms)
52: [ RUN ] GmxApiTest.SystemConstruction
52: Setting the LD random seed to -1311447306
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52: [ OK ] GmxApiTest.SystemConstruction (2315 ms)
52: [ RUN ] GmxApiTest.SaneVersionComparisons
52: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms)
52: [ RUN ] GmxApiTest.VersionNamed0_1_Features
52: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms)
52: [ RUN ] GmxApiTest.RunnerBasicMD
52: Setting the LD random seed to 1587227286
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 2 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.193 0.097 199.3
52: (ns/day) (hour/ns)
52: Performance: 5.231 4.588
52: [ OK ] GmxApiTest.RunnerBasicMD (2426 ms)
52: [ RUN ] GmxApiTest.RunnerReinitialize
52: Setting the LD random seed to -1227235081
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 20 steps, 0.0 ps.
52:
52:
52: Received the remote INT/TERM signal, stopping within 50 steps
52:
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.282 0.141 199.5
52: (ns/day) (hour/ns)
52: Performance: 25.104 0.956
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 20 steps, 0.0 ps.
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.226 0.113 199.3
52: (ns/day) (hour/ns)
52: Performance: 31.234 0.768
52: [ OK ] GmxApiTest.RunnerReinitialize (2591 ms)
52: [ RUN ] GmxApiTest.RunnerContinuedMD
52: Setting the LD random seed to 1452738000
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 10 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.242 0.122 199.4
52: (ns/day) (hour/ns)
52: Performance: 15.270 1.572
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
52: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 20 steps, 0.0 ps.
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.226 0.113 199.3
52: (ns/day) (hour/ns)
52: Performance: 31.293 0.767
52: [ OK ] GmxApiTest.RunnerContinuedMD (2566 ms)
52: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
52: Setting the LD random seed to 1131248191
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
52: Changing nstlist from 10 to 1, rlist from 1.041 to 1
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 1 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.197 0.099 199.3
52: (ns/day) (hour/ns)
52: Performance: 3.414 7.030
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.4-Raspbian-2020.4-2 (single precision)
52: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
52: Changing nstlist from 10 to 1, rlist from 1.041 to 1
52:
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 2 steps, 0.0 ps.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.193 0.097 199.2
52: (ns/day) (hour/ns)
52: Performance: 3.483 6.891
52: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (2533 ms)
52: [----------] 8 tests from GmxApiTest (13430 ms total)
52:
52: [----------] 1 test from GmxApiBasicTest
52: [ RUN ] GmxApiBasicTest.Status
52: [ OK ] GmxApiBasicTest.Status (0 ms)
52: [----------] 1 test from GmxApiBasicTest (0 ms total)
52:
52: [----------] Global test environment tear-down
52: [==========] 9 tests from 2 test cases ran. (13430 ms total)
52: [ PASSED ] 9 tests.
52/54 Test #52: GmxapiMpiTests ...................... Passed 13.46 sec
test 53
Start 53: GmxapiInternalInterfaceTests
53: Test command: /<<PKGBUILDDIR>>/build/basic/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiInternalInterfaceTests.xml"
53: Test timeout computed to be: 600
53: [==========] Running 2 tests from 1 test case.
53: [----------] Global test environment set-up.
53: [----------] 2 tests from GmxApiTest
53: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
53: Setting the LD random seed to 1397617488
53: Generated 331705 of the 331705 non-bonded parameter combinations
53: Generating 1-4 interactions: fudge = 0.5
53: Generated 331705 of the 331705 1-4 parameter combinations
53: Excluding 2 bonded neighbours molecule type 'SOL'
53: Excluding 3 bonded neighbours molecule type 'methane'
53:
53: NOTE 1 [file spc_and_methane.top, line 33]:
53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
53: the time step of 2.0e-03 ps.
53: Maybe you forgot to change the constraints mdp option.
53:
53: Number of degrees of freedom in T-Coupling group System is 18.00
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53: This run will generate roughly 0 Mb of data
53: [ OK ] GmxApiTest.BuildApiWorkflowImpl (842 ms)
53: [ RUN ] GmxApiTest.CreateApiWorkflow
53: Setting the LD random seed to -676726643
53: Generated 331705 of the 331705 non-bonded parameter combinations
53: Generating 1-4 interactions: fudge = 0.5
53: Generated 331705 of the 331705 1-4 parameter combinations
53: Excluding 2 bonded neighbours molecule type 'SOL'
53: Excluding 3 bonded neighbours molecule type 'methane'
53:
53: NOTE 1 [file spc_and_methane.top, line 33]:
53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
53: the time step of 2.0e-03 ps.
53: Maybe you forgot to change the constraints mdp option.
53:
53: Number of degrees of freedom in T-Coupling group System is 18.00
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53: This run will generate roughly 0 Mb of data
53: [ OK ] GmxApiTest.CreateApiWorkflow (833 ms)
53: [----------] 2 tests from GmxApiTest (1675 ms total)
53:
53: [----------] Global test environment tear-down
53: [==========] 2 tests from 1 test case ran. (1675 ms total)
53: [ PASSED ] 2 tests.
53/54 Test #53: GmxapiInternalInterfaceTests ........ Passed 1.70 sec
test 54
Start 54: GmxapiInternalsMpiTests
54: Test command: /<<PKGBUILDDIR>>/build/basic/bin/workflow-details-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiInternalsMpiTests.xml"
54: Test timeout computed to be: 600
54: [==========] Running 2 tests from 1 test case.
54: [----------] Global test environment set-up.
54: [----------] 2 tests from GmxApiTest
54: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
54: Setting the LD random seed to -1910736149
54: Generated 331705 of the 331705 non-bonded parameter combinations
54: Generating 1-4 interactions: fudge = 0.5
54: Generated 331705 of the 331705 1-4 parameter combinations
54: Excluding 2 bonded neighbours molecule type 'SOL'
54: Excluding 3 bonded neighbours molecule type 'methane'
54:
54: NOTE 1 [file spc_and_methane.top, line 33]:
54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
54: the time step of 2.0e-03 ps.
54: Maybe you forgot to change the constraints mdp option.
54:
54: Number of degrees of freedom in T-Coupling group System is 18.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54: This run will generate roughly 0 Mb of data
54: [ OK ] GmxApiTest.BuildApiWorkflowImpl (840 ms)
54: [ RUN ] GmxApiTest.CreateApiWorkflow
54: Setting the LD random seed to 1643189407
54: Generated 331705 of the 331705 non-bonded parameter combinations
54: Generating 1-4 interactions: fudge = 0.5
54: Generated 331705 of the 331705 1-4 parameter combinations
54: Excluding 2 bonded neighbours molecule type 'SOL'
54: Excluding 3 bonded neighbours molecule type 'methane'
54:
54: NOTE 1 [file spc_and_methane.top, line 33]:
54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
54: the time step of 2.0e-03 ps.
54: Maybe you forgot to change the constraints mdp option.
54:
54: Number of degrees of freedom in T-Coupling group System is 18.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54: This run will generate roughly 0 Mb of data
54: [ OK ] GmxApiTest.CreateApiWorkflow (831 ms)
54: [----------] 2 tests from GmxApiTest (1671 ms total)
54:
54: [----------] Global test environment tear-down
54: [==========] 2 tests from 1 test case ran. (1671 ms total)
54: [ PASSED ] 2 tests.
54/54 Test #54: GmxapiInternalsMpiTests ............. Passed 1.69 sec
100% tests passed, 0 tests failed out of 54
Label Time Summary:
GTest = 468.56 sec*proc (54 tests)
IntegrationTest = 177.65 sec*proc (12 tests)
MpiTest = 327.95 sec*proc (8 tests)
SlowTest = 264.12 sec*proc (2 tests)
UnitTest = 26.79 sec*proc (40 tests)
Total Test time (real) = 468.66 sec
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/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so -o ../../../../lib/libgmock.so CMakeFiles/gmock.dir/src/gmock-all.cc.o -lpthread ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/conftest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/conftest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/filematchers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/interactivetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/loggertest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpi_printer.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpi_printer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/refdata.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/refdata_xml.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata_xml.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/simulationdatabase.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/simulationdatabase.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stdiohelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stringtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testasserts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfilemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testinit.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testinit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testmatchers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testoptions.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tprfilegenerator.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energyreader.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energycomparison.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/alignedallocator.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target utility-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mdmodulenotification.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/terminationhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectoryreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdlib-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 70%] Built target testutils-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
/usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 71%] Built target mdrun_test_infrastructure
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target applied_forces-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfitting.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_SingleConstraint_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:331:51: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
331 | std::vector<real> masses = { 1.0, 12.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:333:45: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
333 | std::vector<real> constraintsR0 = { 0.1 };
| ^
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_TwoDisjointConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:377:67: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
377 | std::vector<real> masses = { 0.5, 1.0 / 3.0, 0.25, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:379:50: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
379 | std::vector<real> constraintsR0 = { 2.0, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:384:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
384 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:388:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
388 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:390:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
390 | std::vector<RVec> v = { { 0.0, 1.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 0.0, 0.0, 1.0 }, { 0.0, 0.0, 0.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_ThreeSequentialConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:431:50: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
431 | std::vector<real> constraintsR0 = { 0.1, 0.2 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:438:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
438 | { twoTenthsOverSqrtThree, twoTenthsOverSqrtThree, twoTenthsOverSqrtThree } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:440:101: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
440 | std::vector<RVec> xPrime = { { 0.08, 0.07, 0.01 }, { -0.02, 0.01, -0.02 }, { 0.10, 0.12, 0.11 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:442:85: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
442 | std::vector<RVec> v = { { 1.0, 0.0, 0.0 }, { 0.0, 1.0, 0.0 }, { 0.0, 0.0, 1.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_ThreeConstraintsWithCentralAtom_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:481:61: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
481 | std::vector<real> masses = { 12.0, 1.0, 1.0, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:483:45: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
483 | std::vector<real> constraintsR0 = { 0.1 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:488:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
488 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:493:59: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
493 | { -0.005, 0.011, 0.102 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:495:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
495 | std::vector<RVec> v = { { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_FourSequentialConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:534:67: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
534 | std::vector<real> masses = { 0.5, 1.0 / 3.0, 0.25, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:541:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
541 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:545:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
545 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:547:106: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
547 | std::vector<RVec> v = { { 0.0, 0.0, 2.0 }, { 0.0, 0.0, 3.0 }, { 0.0, 0.0, -4.0 }, { 0.0, 0.0, -1.0 } };
| ^
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::test::ConstraintsTestData::ConstraintsTestData(const string&, int, std::vector<double>, std::vector<int>, std::vector<double>, bool, real (*)[3], bool, float, real, real, const std::vector<gmx::BasicVector<double> >&, const std::vector<gmx::BasicVector<double> >&, const std::vector<gmx::BasicVector<double> >&, real, gmx_bool, int, int, real)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_TriangleOfConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:594:63: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
594 | { 0.0, 0.0, oneTenthOverSqrtTwo } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:596:103: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
596 | std::vector<RVec> xPrime = { { 0.09, -0.02, 0.01 }, { -0.02, 0.10, -0.02 }, { 0.03, -0.01, 0.07 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:598:88: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
598 | std::vector<RVec> v = { { 1.0, 1.0, 1.0 }, { -2.0, -2.0, -2.0 }, { 1.0, 1.0, 1.0 } };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrog.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::{anonymous}::ElectricFieldTest::test(int, real, real, real, real, real)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 72%] Built target applied_forces-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/defaultinitializationallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_grp_tcstat&}; _Tp = t_grp_tcstat; _Alloc = std::allocator<t_grp_tcstat>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_grp_tcstat>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/enumerationhelpers.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::test::LeapFrogTestData::LeapFrogTestData(int, real, const real*, const real*, int, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o
/usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 72%] Built target onlinehelp-test-shared
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
Scanning dependencies of target domdec-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::integrateLeapFrogSimple(gmx::test::LeapFrogTestData*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/fixedcapacityvector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 72%] Built target domdec-test
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
Scanning dependencies of target ewald-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fft-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::test::SettleTestData::SettleTestData(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/block.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<double> gmx::{anonymous}::computeDisplacements(const std::vector<int>&, const std::vector<double>&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest::SetUp()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::{anonymous}::ShakeTest::runTest(size_t, size_t, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsThreeBondsWithCommonAtoms_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoBondsWithACommonAtom_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoDisjointBonds_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsOneBond_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 72%] Built target fft-test
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/gputest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static void gmx::test::{anonymous}::PmeGatherTest::SetUpTestCase()':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:79:80: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
79 | 2.86F, 0.24F, 5.76F, 5.19F, 0.72F };
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:118:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
118 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:146:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
146 | };
| ^
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_butaneUA_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethaneUA_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_methane_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethane_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterThreeSite_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFourSite_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFlexAngle_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_twoMoltypes_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroupsCog_ComputesCogs_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:137:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
137 | updateGroupsCog.addCogs(globalAtomIndices, positions);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:137:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 73%] Built target mdlib-test
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
Scanning dependencies of target hardware-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 73%] Built target hardware-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:57:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
94 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
100 | void runTest(const gmx_gpu_info_t& gpuInfo, ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
206 | runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:57:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
105 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
100 | void runTest(const gmx_gpu_info_t& gpuInfo, ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
206 | runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
Scanning dependencies of target math-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; <template-parameter-2-2> = void; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:653:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
653 | vector(_InputIterator __first, _InputIterator __last,
| ^~~~~~
/usr/include/c++/10/bits/stl_vector.h:653:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:325:81: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
325 | c_sampleCoordinatesFull.begin() + 1);
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:328:81: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
328 | c_sampleCoordinatesFull.begin() + 3);
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:331:83: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
331 | c_sampleCoordinatesFull.begin() + 16);
| ^
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp: In function 'void gmx::test::pmeInitAtoms(gmx_pme_t*, gmx::StatePropagatorDataGpu*, gmx::test::CodePath, const CoordinatesVector&, const ChargesVector&)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp:201:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
201 | stateGpu->copyCoordinatesToGpu(arrayRefFromArray(coordinates.data(), coordinates.size()),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
202 | gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 73%] Built target gpu_utils-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/testhardwarecontexts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_identityTransformation_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:77:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
77 | translateAndScale(toBeTransformed);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_translationWithIdentityScaling_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:84:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
84 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingWithZeroTranslation_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:94:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
94 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_translationAndScalingNonTrivial_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:104:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
104 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingIdentity_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:115:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
115 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingNonTrivial_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:125:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
125 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingInverseNoZero_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:133:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
133 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:134:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
134 | scale.inverseIgnoringZeroScale(testVectors_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingInverseWithOneScaleDimensionZero_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:142:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
142 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:143:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
143 | scale.inverseIgnoringZeroScale(testVectors_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 74%] Built target ewald-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test-shared
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/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 74%] Built target mdrunutility-test-shared
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/gausstransform.cpp
/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdspan-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/accessor_policy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 75%] Built target utility-test
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extents.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extensions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/layouts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/multidimarray.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 76%] Built target onlinehelp-test
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
Scanning dependencies of target options-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/mdspan.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef<gmx::BasicVector<ValueType> >, int) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:69:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
69 | void fillInputContents(ArrayRef<BasicVector<T>> inputRef, int scaleFactor)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
94 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
105 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 77%] Built target mdspan-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pbcutil-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbcenums.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 78%] Built target math-test
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
Scanning dependencies of target random-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 78%] Built target pbcutil-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ExponentialDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
Scanning dependencies of target restraintpotential-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::GammaDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::NormalDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
Scanning dependencies of target table-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 80%] Built target options-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 80%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_InternalCounterSequence_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Default_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Using40Rounds_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Fast_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:117:54: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
117 | const std::vector<uint64_t> bitsZero{ { 0, 0, 0, 0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:127:87: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
127 | 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:136:86: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
136 | 0xa4093822299f31d0ULL, 0x082efa98ec4e6c89ULL } };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
Scanning dependencies of target taskassignment-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color=
Scanning dependencies of target topology-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/exclusionblocks.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_GenerateCanonical_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target random-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/mtop.cpp
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pull-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target taskassignment-test
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
Scanning dependencies of target awh-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target pull-test
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
Scanning dependencies of target simd-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target table-test
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
Scanning dependencies of target compat-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-unused-member-function -o CMakeFiles/compat-test.dir/optional.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/optional.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target topology-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
Scanning dependencies of target gmxana-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::{anonymous}::Entropy::runQuasiHarmonic(real, gmx_bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::{anonymous}::Entropy::runSchlitter(real, gmx_bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, double, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target awh-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/string_view.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/string_view.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 82%] Built target gmxana-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx3-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx2-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 84%] Built target simd-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx1-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 84%] Built target pdb2gmx3-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxpreprocess-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 85%] Built target pdb2gmx2-test
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color=
Scanning dependencies of target correlations-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/optional.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/string_view.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 85%] Built target pdb2gmx1-test
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 86%] Built target compat-test
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target coordinateio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/builder.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacVector_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP2_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP3_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP4_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP1_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacRcross_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP0_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacNormal_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacNoNormalize_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacCos_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genconf.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputPointSet::Value>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputPointSet::Value>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputPointSet::Value>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputPointSet::Value>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValueAndError(int, int, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::test::AnalysisDataTestInputFrame}; _Tp = gmx::test::AnalysisDataTestInputFrame; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputFrame>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputFrame>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'gmx::test::AnalysisDataTestInputFrame& gmx::test::AnalysisDataTestInput::addFrame(real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputFrame*, std::vector<gmx::test::AnalysisDataTestInputFrame> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValueAndError(real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/correlationdataset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/mock_datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genion.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genrestr.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp:51:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void gmx::{anonymous}::ExpfitTest::SetUpTestCase()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadapters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target correlations-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_IndexOutOfRangeInvalid_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_NoNameFromIncorrectTypeNumber_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CorrectNameFromTypeNumber_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_WrongNameNotFound_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CorrectNameFound_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_AddTypeWorks_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_EmptyOnCreate_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_AddMultipleTypesWorks_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CannotAddDuplicateEntry_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target energyanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target energyanalysis-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o
/usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target analysisdata-test-shared
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
Scanning dependencies of target tool-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 88%] Built target gmxpreprocess-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setbothtime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setstarttime.cpp
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fileio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/settimestep.cpp
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
Scanning dependencies of target selection-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp:48:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'testing::Test* testing::internal::ParameterizedTestFactory<TestClass>::CreateTest() [with TestClass = {anonymous}::StructureIORoundtripTest_ReadWriteTpsConf_Test]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/testmodule.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 89%] Built target tool-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 89%] Built target coordinateio-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-modules-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/densityfittingmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp: In member function 'virtual void gmx::test::{anonymous}::MrcDensityMap_ReadsCoordinateTransformationFromFile_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp:110:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
110 | coordinateTransformation({ &coordinate1, &coordinate1 + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp:111:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
111 | coordinateTransformation({ &coordinate2, &coordinate2 + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/domain_decomposition.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const {anonymous}::NeighborhoodSearchTestData::RefPair&}; _Tp = {anonymous}::NeighborhoodSearchTestData::RefPair; _Alloc = std::allocator<{anonymous}::NeighborhoodSearchTestData::RefPair>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In function 'void {anonymous}::NeighborhoodSearchTestData::computeReferencesInternal(t_pbc*, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double*&}; _Tp = {anonymous}::NeighborhoodSearchTestData::TestPosition; _Alloc = std::allocator<{anonymous}::NeighborhoodSearchTestData::TestPosition>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void {anonymous}::NeighborhoodSearchTestData::useRefPositionsAsTestPositions()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'gmx::AnalysisNeighborhoodPositions {anonymous}::NeighborhoodSearchTestData::testPositions() const':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void {anonymous}::NeighborhoodSearchTest::testPairSearch(gmx::AnalysisNeighborhoodSearch*, const {anonymous}::NeighborhoodSearchTestData&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::BasicVector<double>}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void {anonymous}::NeighborhoodSearchTest::testPairSearchIndexed(gmx::AnalysisNeighborhood*, const {anonymous}::NeighborhoodSearchTestData&, uint64_t)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformNoOriginGiven_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:87:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
87 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomTestPositions(int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomTestPositions(int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomRefPositions(int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchExclusions_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformWithOriginDefined_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:106:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
106 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSelfPairsSearch_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static const {anonymous}::NeighborhoodSearchTestData& {anonymous}::RandomBoxXYFullPBCData::get()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformWithStartValues_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:124:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
124 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchTriclinic_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearch2DPBC_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSearch_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchBox_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSearchExclusions_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesSkippingPairs_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSelfPairsSearch_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesConcurrentSearches_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesNullPBC_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesNoPBC_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 89%] Built target mdrun-modules-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/fileioxdrserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-coordination-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/periodicactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 90%] Built target fileio-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 90%] Built target mdrun-mpi-coordination-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-io-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/exactcontinuation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 91%] Built target mdrun-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/dispersion_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 91%] Built target selection-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-output-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-non-integrator-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-io-test.dir/termination.cpp.o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 92%] Built target mdrun-io-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/outputfiles.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/simulator.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/normalmodes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target mdrun-output-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-tpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target mdrun-tpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simple_mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/simulator.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 94%] Built target mdrun-test
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-mpi-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
[ 94%] Built target workflow-details-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 94%] Built target mdrun-non-integrator-test
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-test.dir/workflow.cpp.o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target workflow-details-test
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
Scanning dependencies of target commandline-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target gmxapi-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-test.dir/status.cpp.o CMakeFiles/gmxapi-test.dir/system.cpp.o CMakeFiles/gmxapi-test.dir/version.cpp.o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-test.dir/runner.cpp.o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target gmxapi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 97%] Built target commandline-test
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target trajectoryanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 97%] Built target mdrunutility-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 97%] Built target mdrunutility-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/average.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/sasa.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 97%] Built target analysisdata-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'void {anonymous}::SurfaceAreaTest::generateRandomPositions(int)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesSinglePoint_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPoints_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPointsOfUnequalRadius_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints12_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints32_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints42_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints122_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target trajectoryanalysis-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
(cd build/basic-dp; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic-dp/lib ctest -V || dpkg-architecture -i hurd-i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic-dp
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: TestUtilsUnitTests
1: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml"
1: Test timeout computed to be: 30
1: [==========] Running 59 tests from 5 test cases.
1: [----------] Global test environment set-up.
1: [----------] 10 tests from InteractiveTestHelperTest
1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (1 ms)
1: [----------] 10 tests from InteractiveTestHelperTest (15 ms total)
1:
1: [----------] 34 tests from ReferenceDataTest
1: [ RUN ] ReferenceDataTest.HandlesSimpleData
1: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringBlockData
1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesVectorData
1: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceData
1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectData
1: [ OK ] ReferenceDataTest.HandlesIncorrectData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingData
1: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedData
1: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnys
1: [ OK ] ReferenceDataTest.HandlesAnys (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesReadingValues
1: [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms)
1: [----------] 34 tests from ReferenceDataTest (26 ms total)
1:
1: [----------] 7 tests from FloatingPointDifferenceTest
1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total)
1:
1: [----------] 4 tests from FloatingPointToleranceTest
1: [ RUN ] FloatingPointToleranceTest.UlpTolerance
1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total)
1:
1: [----------] 4 tests from XvgTests
1: [ RUN ] XvgTests.CreateFile
1: [ OK ] XvgTests.CreateFile (2 ms)
1: [ RUN ] XvgTests.CheckMissing
1: [ OK ] XvgTests.CheckMissing (1 ms)
1: [ RUN ] XvgTests.CheckExtra
1: [ OK ] XvgTests.CheckExtra (1 ms)
1: [ RUN ] XvgTests.ReadIncorrect
1: [ OK ] XvgTests.ReadIncorrect (2 ms)
1: [----------] 4 tests from XvgTests (6 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 59 tests from 5 test cases ran. (47 ms total)
1: [ PASSED ] 59 tests.
1/54 Test #1: TestUtilsUnitTests .................. Passed 0.07 sec
test 2
Start 2: TestUtilsMpiUnitTests
2: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml"
2: Test timeout computed to be: 30
2: [==========] Running 1 test from 1 test case.
2: [----------] Global test environment set-up.
2: [----------] 1 test from MpiSelfTest
2: [ RUN ] MpiSelfTest.Runs
2: [ OK ] MpiSelfTest.Runs (0 ms)
2: [----------] 1 test from MpiSelfTest (0 ms total)
2:
2: [----------] Global test environment tear-down
2: [==========] 1 test from 1 test case ran. (0 ms total)
2: [ PASSED ] 1 test.
2/54 Test #2: TestUtilsMpiUnitTests ............... Passed 0.02 sec
test 3
Start 3: UtilityUnitTests
3: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml"
3: Test timeout computed to be: 30
3: [==========] Running 347 tests from 56 test cases.
3: [----------] Global test environment set-up.
3: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.Move
3: [ OK ] AllocatorTest/0.Move (0 ms)
3: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/0 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<double, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.Move
3: [ OK ] AllocatorTest/1.Move (0 ms)
3: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/1 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.Move
3: [ OK ] AllocatorTest/2.Move (0 ms)
3: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/2 (0 ms total)
3:
3: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.Move
3: [ OK ] AllocatorTest/3.Move (0 ms)
3: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/3 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.Move
3: [ OK ] AllocatorTest/4.Move (0 ms)
3: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/4 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.Move
3: [ OK ] AllocatorTest/5.Move (0 ms)
3: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/5 (1 ms total)
3:
3: [----------] 1 test from AllocatorUntypedTest
3: [ RUN ] AllocatorUntypedTest.Comparison
3: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
3: [----------] 1 test from AllocatorUntypedTest (0 ms total)
3:
3: [----------] 1 test from EmptyArrayRefTest
3: [ RUN ] EmptyArrayRefTest.IsEmpty
3: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyArrayRefTest (0 ms total)
3:
3: [----------] 1 test from EmptyConstArrayRefTest
3: [ RUN ] EmptyConstArrayRefTest.IsEmpty
3: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
3: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/0 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
3: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/1 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
3: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/2 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
3: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (1 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/3 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
3: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (1 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/4 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
3: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (1 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/5 (2 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
3: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (1 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/6 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
3: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/7 (2 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
3: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (1 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/8 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
3: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (1 ms)
3: [----------] 9 tests from ArrayRefTest/9 (2 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
3: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (1 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/10 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
3: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (1 ms)
3: [----------] 9 tests from ArrayRefTest/11 (2 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
3: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/12 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
3: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (1 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (1 ms)
3: [----------] 9 tests from ArrayRefTest/13 (2 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
3: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/14 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
3: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (1 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (1 ms)
3: [----------] 9 tests from ArrayRefTest/15 (2 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
3: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/16 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
3: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (1 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/17 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
3: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (1 ms)
3: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/18 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
3: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/19 (0 ms total)
3:
3: [----------] 2 tests from CStringUtilityTest
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms)
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms)
3: [----------] 2 tests from CStringUtilityTest (0 ms total)
3:
3: [----------] 2 tests from DefaultInitializationAllocator
3: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms)
3: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms)
3: [----------] 2 tests from DefaultInitializationAllocator (0 ms total)
3:
3: [----------] 4 tests from EnumerationHelpersTest
3: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks
3: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe
3: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms)
3: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms)
3: [----------] 4 tests from EnumerationHelpersTest (0 ms total)
3:
3: [----------] 9 tests from FixedCapacityVectorTest
3: [ RUN ] FixedCapacityVectorTest.IsEmpty
3: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PushWorks
3: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PopWorks
3: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ClearWorks
3: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks
3: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.AtThrows
3: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms)
3: [ RUN ] FixedCapacityVectorTest.IteratorWorks
3: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks
3: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks
3: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms)
3: [----------] 9 tests from FixedCapacityVectorTest (0 ms total)
3:
3: [----------] 5 tests from InMemorySerializerTest
3: [ RUN ] InMemorySerializerTest.Roundtrip
3: [ OK ] InMemorySerializerTest.Roundtrip (1 ms)
3: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap
3: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SizeIsCorrect
3: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms)
3: [----------] 5 tests from InMemorySerializerTest (1 ms total)
3:
3: [----------] 4 tests from KeyValueTreeSerializerTest
3: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
3: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms)
3: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
3: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (1 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms)
3: [----------] 4 tests from KeyValueTreeSerializerTest (1 ms total)
3:
3: [----------] 6 tests from TreeValueTransformTest
3: [ RUN ] TreeValueTransformTest.SimpleTransforms
3: [ OK ] TreeValueTransformTest.SimpleTransforms (1 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
3: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
3: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromString
3: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
3: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (1 ms)
3: [ RUN ] TreeValueTransformTest.ScopedTransformRules
3: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms)
3: [----------] 6 tests from TreeValueTransformTest (2 ms total)
3:
3: [----------] 1 test from TreeValueTransformErrorTest
3: [ RUN ] TreeValueTransformErrorTest.ConversionError
3: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms)
3: [----------] 1 test from TreeValueTransformErrorTest (0 ms total)
3:
3: [----------] 7 tests from LoggerTest
3: [ RUN ] LoggerTest.EmptyLoggerWorks
3: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
3: [ RUN ] LoggerTest.LogsToStream
3: [ OK ] LoggerTest.LogsToStream (0 ms)
3: [ RUN ] LoggerTest.LogsToFile
3: [ OK ] LoggerTest.LogsToFile (0 ms)
3: [ RUN ] LoggerTest.LevelFilteringWorks
3: [ OK ] LoggerTest.LevelFilteringWorks (1 ms)
3: [ RUN ] LoggerTest.LogsToMultipleStreams
3: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms)
3: [ RUN ] LoggerTest.LogsToMultipleFiles
3: [ OK ] LoggerTest.LogsToMultipleFiles (1 ms)
3: [ RUN ] LoggerTest.LogsToStreamAndFile
3: [ OK ] LoggerTest.LogsToStreamAndFile (1 ms)
3: [----------] 7 tests from LoggerTest (4 ms total)
3:
3: [----------] 4 tests from MutexBasicTest
3: [ RUN ] MutexBasicTest.CanBeMade
3: [ OK ] MutexBasicTest.CanBeMade (0 ms)
3: [ RUN ] MutexBasicTest.CanBeLocked
3: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeTryLocked
3: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
3: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
3: [----------] 4 tests from MutexBasicTest (0 ms total)
3:
3: [----------] 3 tests from MutexTaskTest
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (1 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
3: [----------] 3 tests from MutexTaskTest (1 ms total)
3:
3: [----------] 2 tests from PathTest
3: [ RUN ] PathTest.StripSourcePrefixWorks
3: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
3: [ RUN ] PathTest.SearchOperationsWork
3: [ OK ] PathTest.SearchOperationsWork (1 ms)
3: [----------] 2 tests from PathTest (1 ms total)
3:
3: [----------] 2 tests from PhysicalNodeCommunicatorTest
3: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
3: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
3: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
3: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
3: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
3:
3: [----------] 9 tests from StringUtilityTest
3: [ RUN ] StringUtilityTest.StartsWith
3: [ OK ] StringUtilityTest.StartsWith (0 ms)
3: [ RUN ] StringUtilityTest.EndsWith
3: [ OK ] StringUtilityTest.EndsWith (0 ms)
3: [ RUN ] StringUtilityTest.StripSuffixIfPresent
3: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms)
3: [ RUN ] StringUtilityTest.StripString
3: [ OK ] StringUtilityTest.StripString (0 ms)
3: [ RUN ] StringUtilityTest.SplitString
3: [ OK ] StringUtilityTest.SplitString (0 ms)
3: [ RUN ] StringUtilityTest.SplitDelimitedString
3: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms)
3: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
3: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms)
3: [----------] 9 tests from StringUtilityTest (3 ms total)
3:
3: [----------] 2 tests from FormatStringTest
3: [ RUN ] FormatStringTest.HandlesBasicFormatting
3: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
3: [ RUN ] FormatStringTest.HandlesLongStrings
3: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
3: [----------] 2 tests from FormatStringTest (0 ms total)
3:
3: [----------] 1 test from StringFormatterTest
3: [ RUN ] StringFormatterTest.HandlesBasicFormatting
3: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
3: [----------] 1 test from StringFormatterTest (0 ms total)
3:
3: [----------] 1 test from formatAndJoinTest
3: [ RUN ] formatAndJoinTest.Works
3: [ OK ] formatAndJoinTest.Works (0 ms)
3: [----------] 1 test from formatAndJoinTest (0 ms total)
3:
3: [----------] 1 test from JoinStringsTest
3: [ RUN ] JoinStringsTest.Works
3: [ OK ] JoinStringsTest.Works (0 ms)
3: [----------] 1 test from JoinStringsTest (0 ms total)
3:
3: [----------] 6 tests from ReplaceAllTest
3: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
3: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesNoMatches
3: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
3: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
3: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
3: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
3: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
3: [----------] 6 tests from ReplaceAllTest (1 ms total)
3:
3: [----------] 10 tests from TextLineWrapperTest
3: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
3: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
3: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
3: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectly
3: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (1 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndent
3: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
3: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
3: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
3: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms)
3: [----------] 10 tests from TextLineWrapperTest (2 ms total)
3:
3: [----------] 6 tests from TextWriterTest
3: [ RUN ] TextWriterTest.WritesLines
3: [ OK ] TextWriterTest.WritesLines (0 ms)
3: [ RUN ] TextWriterTest.WritesLinesInParts
3: [ OK ] TextWriterTest.WritesLinesInParts (0 ms)
3: [ RUN ] TextWriterTest.WritesWrappedLines
3: [ OK ] TextWriterTest.WritesWrappedLines (0 ms)
3: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
3: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms)
3: [ RUN ] TextWriterTest.TracksNewlines
3: [ OK ] TextWriterTest.TracksNewlines (0 ms)
3: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
3: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms)
3: [----------] 6 tests from TextWriterTest (1 ms total)
3:
3: [----------] 1 test from TypeTraitsTest
3: [ RUN ] TypeTraitsTest.IsIntegralConstant
3: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
3: [----------] 1 test from TypeTraitsTest (0 ms total)
3:
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (1 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (1 ms total)
3:
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total)
3:
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (1 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (1 ms total)
3:
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (1 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (1 ms total)
3:
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms)
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (3 ms total)
3:
3: [----------] Global test environment tear-down
3: [==========] 347 tests from 56 test cases ran. (53 ms total)
3: [ PASSED ] 347 tests.
3/54 Test #3: UtilityUnitTests .................... Passed 0.11 sec
test 4
Start 4: UtilityMpiUnitTests
4: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml"
4: Test timeout computed to be: 30
4: [==========] Running 2 tests from 1 test case.
4: [----------] Global test environment set-up.
4: [----------] 2 tests from PhysicalNodeCommunicatorTest
4: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
4: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (1 ms)
4: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
4: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (1 ms)
4: [----------] 2 tests from PhysicalNodeCommunicatorTest (2 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 2 tests from 1 test case ran. (2 ms total)
4: [ PASSED ] 2 tests.
4/54 Test #4: UtilityMpiUnitTests ................. Passed 0.02 sec
test 5
Start 5: MdlibUnitTest
5: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml"
5: Test timeout computed to be: 30
5: [==========] Running 149 tests from 11 test cases.
5: [----------] Global test environment set-up.
5: [----------] 1 test from VerletBufferConstraintTest
5: [ RUN ] VerletBufferConstraintTest.EqualMasses
5: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms)
5: [----------] 1 test from VerletBufferConstraintTest (0 ms total)
5:
5: [----------] 2 tests from PrEbinTest
5: [ RUN ] PrEbinTest.HandlesAverages
5: [ OK ] PrEbinTest.HandlesAverages (1 ms)
5: [ RUN ] PrEbinTest.HandlesEmptyAverages
5: [ OK ] PrEbinTest.HandlesEmptyAverages (0 ms)
5: [----------] 2 tests from PrEbinTest (1 ms total)
5:
5: [----------] 4 tests from ShakeTest
5: [ RUN ] ShakeTest.ConstrainsOneBond
5: [ OK ] ShakeTest.ConstrainsOneBond (0 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
5: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
5: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms)
5: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
5: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (1 ms)
5: [----------] 4 tests from ShakeTest (1 ms total)
5:
5: [----------] 1 test from NullSignalTest
5: [ RUN ] NullSignalTest.NullSignallerWorks
5: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
5: [----------] 1 test from NullSignalTest (0 ms total)
5:
5: [----------] 7 tests from SignalTest
5: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
5: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
5: [----------] 7 tests from SignalTest (0 ms total)
5:
5: [----------] 9 tests from UpdateGroups
5: [ RUN ] UpdateGroups.ethaneUA
5: [ OK ] UpdateGroups.ethaneUA (0 ms)
5: [ RUN ] UpdateGroups.methane
5: [ OK ] UpdateGroups.methane (0 ms)
5: [ RUN ] UpdateGroups.ethane
5: [ OK ] UpdateGroups.ethane (0 ms)
5: [ RUN ] UpdateGroups.butaneUA
5: [ OK ] UpdateGroups.butaneUA (0 ms)
5: [ RUN ] UpdateGroups.waterThreeSite
5: [ OK ] UpdateGroups.waterThreeSite (1 ms)
5: [ RUN ] UpdateGroups.waterFourSite
5: [ OK ] UpdateGroups.waterFourSite (0 ms)
5: [ RUN ] UpdateGroups.fourAtomsWithSettle
5: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
5: [ RUN ] UpdateGroups.waterFlexAngle
5: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
5: [ RUN ] UpdateGroups.twoMoltypes
5: [ OK ] UpdateGroups.twoMoltypes (0 ms)
5: [----------] 9 tests from UpdateGroups (1 ms total)
5:
5: [----------] 1 test from UpdateGroupsCog
5: [ RUN ] UpdateGroupsCog.ComputesCogs
5: [ OK ] UpdateGroupsCog.ComputesCogs (1 ms)
5: [----------] 1 test from UpdateGroupsCog (1 ms total)
5:
5: [----------] 84 tests from WithParameters/ConstraintsTest
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/2
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/3
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/20
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/21
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/22
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/23
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 (0 ms)
5: [----------] 84 tests from WithParameters/ConstraintsTest (11 ms total)
5:
5: [----------] 11 tests from WithParameters/EnergyOutputTest
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (8 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (5 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (8 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3
5: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (2 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file
5:
Reading energy frame 0 time 10.100
Reading energy frame 1 time 27.500
Reading energy frame 2 time 44.900
Reading energy frame 3 time 62.300
Reading energy frame 4 time 79.700
Reading energy frame 5 time 97.100
Reading energy frame 6 time 114.500
Reading energy frame 7 time 131.900
Reading energy frame 8 time 149.300
Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (28 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (8 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (9 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (9 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (9 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (9 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (9 ms)
5: [----------] 11 tests from WithParameters/EnergyOutputTest (111 ms total)
5:
5: [----------] 16 tests from WithParameters/LeapFrogTest
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (2 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (8 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (2 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (3 ms)
5: [----------] 16 tests from WithParameters/LeapFrogTest (40 ms total)
5:
5: [----------] 13 tests from WithParameters/SettleTest
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (2 ms)
5: [----------] 13 tests from WithParameters/SettleTest (15 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 149 tests from 11 test cases ran. (181 ms total)
5: [ PASSED ] 149 tests.
5/54 Test #5: MdlibUnitTest ....................... Passed 0.21 sec
test 6
Start 6: AppliedForcesUnitTest
6: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml"
6: Test timeout computed to be: 30
6: [==========] Running 20 tests from 4 test cases.
6: [----------] Global test environment set-up.
6: [----------] 2 tests from DensityFittingTest
6: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows
6: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (1 ms)
6: [ RUN ] DensityFittingTest.SingleAtom
6: [ OK ] DensityFittingTest.SingleAtom (0 ms)
6: [----------] 2 tests from DensityFittingTest (1 ms total)
6:
6: [----------] 8 tests from DensityFittingOptionsTest
6: [ RUN ] DensityFittingOptionsTest.DefaultParameters
6: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OptionSetsActive
6: [ OK ] DensityFittingOptionsTest.OptionSetsActive (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive
6: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive
6: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (0 ms)
6: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup
6: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (1 ms)
6: [ RUN ] DensityFittingOptionsTest.InternalsToKvt
6: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms)
6: [ RUN ] DensityFittingOptionsTest.KvtToInternal
6: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms)
6: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent
6: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (0 ms)
6: [----------] 8 tests from DensityFittingOptionsTest (1 ms total)
6:
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest
6: [ RUN ] DensityFittingAmplitudeLookupTest.Unity
6: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Charge
6: [ OK ] DensityFittingAmplitudeLookupTest.Charge (1 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Masses
6: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms)
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest (1 ms total)
6:
6: [----------] 3 tests from ElectricFieldTest
6: [ RUN ] ElectricFieldTest.Static
6: [ OK ] ElectricFieldTest.Static (0 ms)
6: [ RUN ] ElectricFieldTest.Oscillating
6: [ OK ] ElectricFieldTest.Oscillating (0 ms)
6: [ RUN ] ElectricFieldTest.Pulsed
6: [ OK ] ElectricFieldTest.Pulsed (0 ms)
6: [----------] 3 tests from ElectricFieldTest (0 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 20 tests from 4 test cases ran. (4 ms total)
6: [ PASSED ] 20 tests.
6/54 Test #6: AppliedForcesUnitTest ............... Passed 0.02 sec
test 7
Start 7: CommandLineUnitTests
7: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml"
7: Test timeout computed to be: 30
7: [==========] Running 59 tests from 7 test cases.
7: [----------] Global test environment set-up.
7: [----------] 3 tests from CommandLineHelpModuleTest
7: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
7: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms)
7: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
7: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms)
7: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
7: [ OK ] CommandLineHelpModuleTest.ExportsHelp (3 ms)
7: [----------] 3 tests from CommandLineHelpModuleTest (5 ms total)
7:
7: [----------] 7 tests from CommandLineHelpWriterTest
7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
7: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (1 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
7: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
7: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (1 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
7: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
7: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (1 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
7: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues
7: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (0 ms)
7: [----------] 7 tests from CommandLineHelpWriterTest (3 ms total)
7:
7: [----------] 6 tests from CommandLineModuleManagerTest
7: [ RUN ] CommandLineModuleManagerTest.RunsModule
7: [ OK ] CommandLineModuleManagerTest.RunsModule (1 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (1 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (1 ms)
7: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
7: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms)
7: [----------] 6 tests from CommandLineModuleManagerTest (3 ms total)
7:
7: [----------] 13 tests from CommandLineParserTest
7: [ RUN ] CommandLineParserTest.HandlesSingleValues
7: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
7: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
7: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
7: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
7: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
7: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesString
7: [ OK ] CommandLineParserTest.HandlesString (0 ms)
7: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
7: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
7: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
7: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
7: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
7: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
7: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms)
7: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
7: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
7: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
7: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms)
7: [----------] 13 tests from CommandLineParserTest (2 ms total)
7:
7: [----------] 6 tests from CommandLineProgramContextTest
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (1 ms)
7: [----------] 6 tests from CommandLineProgramContextTest (1 ms total)
7:
7: [----------] 3 tests from OutputNamesTest
7: [ RUN ] OutputNamesTest.CanBeSuffixed
7: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms)
7: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend
7: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms)
7: [ RUN ] OutputNamesTest.CanHavePartNumberAdded
7: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms)
7: [----------] 3 tests from OutputNamesTest (0 ms total)
7:
7: [----------] 21 tests from ParseCommonArgsTest
7: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
7: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
7: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
7: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
7: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
7: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
7: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (1 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
7: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
7: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
7: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
7: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
7: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
7: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms)
7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
7: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (1 ms)
7: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
7: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms)
7: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
7: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (1 ms)
7: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
7: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms)
7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms)
7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (1 ms)
7: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
7: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms)
7: [----------] 21 tests from ParseCommonArgsTest (6 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 59 tests from 7 test cases ran. (20 ms total)
7: [ PASSED ] 59 tests.
7/54 Test #7: CommandLineUnitTests ................ Passed 0.04 sec
test 8
Start 8: DomDecTests
8: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/DomDecTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 9 tests from 2 test cases.
8: [----------] Global test environment set-up.
8: [----------] 7 tests from HashedMap
8: [ RUN ] HashedMap.InsertsFinds
8: [ OK ] HashedMap.InsertsFinds (0 ms)
8: [ RUN ] HashedMap.NegativeKeysWork
8: [ OK ] HashedMap.NegativeKeysWork (0 ms)
8: [ RUN ] HashedMap.InsertsErases
8: [ OK ] HashedMap.InsertsErases (0 ms)
8: [ RUN ] HashedMap.InsertsOrAssigns
8: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
8: [ RUN ] HashedMap.Clears
8: [ OK ] HashedMap.Clears (0 ms)
8: [ RUN ] HashedMap.LinkedEntries
8: [ OK ] HashedMap.LinkedEntries (0 ms)
8: [ RUN ] HashedMap.ResizesTable
8: [ OK ] HashedMap.ResizesTable (0 ms)
8: [----------] 7 tests from HashedMap (0 ms total)
8:
8: [----------] 2 tests from LocalAtomSetManager
8: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
8: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms)
8: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
8: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (1 ms)
8: [----------] 2 tests from LocalAtomSetManager (1 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 9 tests from 2 test cases ran. (1 ms total)
8: [ PASSED ] 9 tests.
8/54 Test #8: DomDecTests ......................... Passed 0.02 sec
test 9
Start 9: EwaldUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 257 tests from 10 test cases.
9: [----------] Global test environment set-up.
9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (1 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (5 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms)
9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (6 ms total)
9:
9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (4 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (10 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (5 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (6 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (5 ms)
9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (143 ms total)
9:
9: [----------] 144 tests from SaneInput/PmeGatherTest
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (0 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (1 ms)
9: [----------] 144 tests from SaneInput/PmeGatherTest (143 ms total)
9:
9: [----------] 16 tests from SaneInput/PmeSolveTest
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (3 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (3 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (3 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (1 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (3 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (3 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (2 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (3 ms)
9: [----------] 16 tests from SaneInput/PmeSolveTest (49 ms total)
9:
9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (2 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (2 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (2 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (2 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (2 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (2 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (2 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (2 ms)
9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (17 ms total)
9:
9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (4 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (4 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (3 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (3 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (4 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (5 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (2 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (2 ms)
9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (28 ms total)
9:
9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (3 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (1 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (3 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (3 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (2 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (5 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (1 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (3 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (1 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (2 ms)
9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (47 ms total)
9:
9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (2 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (5 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (3 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (4 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (4 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (5 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (2 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (3 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (3 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (4 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (5 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (5 ms)
9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (50 ms total)
9:
9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (3 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (4 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (4 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (5 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (5 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (6 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (3 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (3 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (4 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (5 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (7 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (7 ms)
9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (65 ms total)
9:
9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (8 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (9 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (13 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (15 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (19 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (22 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (8 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (10 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (12 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (14 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (17 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (20 ms)
9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (204 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 257 tests from 10 test cases ran. (777 ms total)
9: [ PASSED ] 257 tests.
9/54 Test #9: EwaldUnitTests ...................... Passed 0.87 sec
test 10
Start 10: FFTUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/FFTUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 14 tests from 4 test cases.
10: [----------] Global test environment set-up.
10: [----------] 2 tests from ManyFFTTest
10: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
10: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (7 ms)
10: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
10: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (11 ms)
10: [----------] 2 tests from ManyFFTTest (18 ms total)
10:
10: [----------] 1 test from FFTTest
10: [ RUN ] FFTTest.Real2DLength18_15Test
10: [ OK ] FFTTest.Real2DLength18_15Test (4 ms)
10: [----------] 1 test from FFTTest (4 ms total)
10:
10: [----------] 1 test from FFFTest3D
10: [ RUN ] FFFTest3D.Real5_6_9
10: [ OK ] FFFTest3D.Real5_6_9 (3 ms)
10: [----------] 1 test from FFFTest3D (4 ms total)
10:
10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (2 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (2 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (6 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (10 ms)
10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (25 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 14 tests from 4 test cases ran. (51 ms total)
10: [ PASSED ] 14 tests.
10/54 Test #10: FFTUnitTests ........................ Passed 0.07 sec
test 11
Start 11: GpuUtilsUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 62 tests from 20 test cases.
11: [----------] Global test environment set-up.
11: [----------] 2 tests from ClfftInitializer
11: [ RUN ] ClfftInitializer.SingleInitializationWorks
11: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms)
11: [ RUN ] ClfftInitializer.TwoInitializationsWork
11: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms)
11: [----------] 2 tests from ClfftInitializer (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
11: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/0 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double
11: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/1 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<double>
11: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
11: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/3 (0 ms total)
11:
11: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
11: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
11: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
11: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
11: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
11: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total)
11:
11: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double
11: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
11: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
11: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
11: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
11: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total)
11:
11: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<double>
11: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
11: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
11: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
11: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
11: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
11: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
11: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.Swap
11: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.Comparison
11: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double
11: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
11: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.Swap
11: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.Comparison
11: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/1 (1 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<double>
11: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
11: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.Swap
11: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.Comparison
11: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
11: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
11: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.Swap
11: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.Comparison
11: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double
11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<double>
11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (1 ms)
11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (1 ms total)
11:
11: [----------] 1 test from HostAllocatorUntypedTest
11: [ RUN ] HostAllocatorUntypedTest.Comparison
11: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
11: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
11:
11: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/0.Move
11: [ OK ] AllocatorTest/0.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/0 (0 ms total)
11:
11: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/1.Move
11: [ OK ] AllocatorTest/1.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/1 (1 ms total)
11:
11: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/2.Move
11: [ OK ] AllocatorTest/2.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/2 (0 ms total)
11:
11: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/3.Move
11: [ OK ] AllocatorTest/3.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/3 (1 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 62 tests from 20 test cases ran. (5 ms total)
11: [ PASSED ] 62 tests.
11/54 Test #11: GpuUtilsUnitTests ................... Passed 0.03 sec
test 12
Start 12: HardwareUnitTests
12: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml"
12: Test timeout computed to be: 30
12: [==========] Running 4 tests from 1 test case.
12: [----------] Global test environment set-up.
12: [----------] 4 tests from HardwareTopologyTest
12: [ RUN ] HardwareTopologyTest.Execute
12: [ OK ] HardwareTopologyTest.Execute (18 ms)
12: [ RUN ] HardwareTopologyTest.HwlocExecute
12: [ OK ] HardwareTopologyTest.HwlocExecute (16 ms)
12: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
12: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (19 ms)
12: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
12: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (16 ms)
12: [----------] 4 tests from HardwareTopologyTest (69 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 4 tests from 1 test case ran. (70 ms total)
12: [ PASSED ] 4 tests.
12/54 Test #12: HardwareUnitTests ................... Passed 0.09 sec
test 13
Start 13: MathUnitTests
13: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MathUnitTests.xml"
13: Test timeout computed to be: 30
13: [==========] Running 204 tests from 29 test cases.
13: [----------] Global test environment set-up.
13: [----------] 1 test from EmptyArrayRefWithPaddingTest
13: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
13: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
13: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total)
13:
13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
13: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
13: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total)
13:
13: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
13: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
13: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
13: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
13: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
13: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total)
13:
13: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
13: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
13: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
13: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
13: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
13: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total)
13:
13: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
13: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
13: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
13: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
13: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
13: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total)
13:
13: [----------] 8 tests from TranslateAndScaleTest
13: [ RUN ] TranslateAndScaleTest.identityTransformation
13: [ OK ] TranslateAndScaleTest.identityTransformation (0 ms)
13: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling
13: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (1 ms)
13: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation
13: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms)
13: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial
13: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingIdentity
13: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingNonTrivial
13: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero
13: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero
13: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms)
13: [----------] 8 tests from TranslateAndScaleTest (2 ms total)
13:
13: [----------] 12 tests from DensitySimilarityTest
13: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect
13: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect
13: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch
13: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms)
13: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch
13: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms)
13: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect
13: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero
13: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms)
13: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect
13: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect
13: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne
13: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (71 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated
13: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (72 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated
13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (143 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect
13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms)
13: [----------] 12 tests from DensitySimilarityTest (287 ms total)
13:
13: [----------] 6 tests from StructureSimilarityTest
13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
13: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
13: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
13: [----------] 6 tests from StructureSimilarityTest (0 ms total)
13:
13: [----------] 8 tests from ExponentialMovingAverage
13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero
13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms)
13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative
13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms)
13: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue
13: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms)
13: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue
13: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms)
13: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly
13: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms)
13: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing
13: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms)
13: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect
13: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms)
13: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree
13: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms)
13: [----------] 8 tests from ExponentialMovingAverage (1 ms total)
13:
13: [----------] 21 tests from FunctionTest
13: [ RUN ] FunctionTest.StaticLog2
13: [ OK ] FunctionTest.StaticLog2 (0 ms)
13: [ RUN ] FunctionTest.Log2I32Bit
13: [ OK ] FunctionTest.Log2I32Bit (0 ms)
13: [ RUN ] FunctionTest.Log2I64Bit
13: [ OK ] FunctionTest.Log2I64Bit (1 ms)
13: [ RUN ] FunctionTest.GreatestCommonDivisor
13: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
13: [ RUN ] FunctionTest.InvsqrtFloat
13: [ OK ] FunctionTest.InvsqrtFloat (0 ms)
13: [ RUN ] FunctionTest.InvsqrtDouble
13: [ OK ] FunctionTest.InvsqrtDouble (0 ms)
13: [ RUN ] FunctionTest.InvsqrtInteger
13: [ OK ] FunctionTest.InvsqrtInteger (1 ms)
13: [ RUN ] FunctionTest.InvcbrtFloat
13: [ OK ] FunctionTest.InvcbrtFloat (0 ms)
13: [ RUN ] FunctionTest.InvcbrtDouble
13: [ OK ] FunctionTest.InvcbrtDouble (0 ms)
13: [ RUN ] FunctionTest.InvcbrtInteger
13: [ OK ] FunctionTest.InvcbrtInteger (0 ms)
13: [ RUN ] FunctionTest.SixthrootFloat
13: [ OK ] FunctionTest.SixthrootFloat (0 ms)
13: [ RUN ] FunctionTest.SixthrootDouble
13: [ OK ] FunctionTest.SixthrootDouble (1 ms)
13: [ RUN ] FunctionTest.SixthrootInteger
13: [ OK ] FunctionTest.SixthrootInteger (0 ms)
13: [ RUN ] FunctionTest.InvsixthrootFloat
13: [ OK ] FunctionTest.InvsixthrootFloat (0 ms)
13: [ RUN ] FunctionTest.InvsixthrootDouble
13: [ OK ] FunctionTest.InvsixthrootDouble (0 ms)
13: [ RUN ] FunctionTest.InvsixthrootInteger
13: [ OK ] FunctionTest.InvsixthrootInteger (0 ms)
13: [ RUN ] FunctionTest.Powers
13: [ OK ] FunctionTest.Powers (0 ms)
13: [ RUN ] FunctionTest.ErfInvFloat
13: [ OK ] FunctionTest.ErfInvFloat (1 ms)
13: [ RUN ] FunctionTest.ErfInvDouble
13: [ OK ] FunctionTest.ErfInvDouble (0 ms)
13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
13: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms)
13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
13: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms)
13: [----------] 21 tests from FunctionTest (5 ms total)
13:
13: [----------] 4 tests from GaussianOn1DLattice
13: [ RUN ] GaussianOn1DLattice.sumsCloseToOne
13: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms)
13: [ RUN ] GaussianOn1DLattice.isCorrect
13: [ OK ] GaussianOn1DLattice.isCorrect (0 ms)
13: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero
13: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms)
13: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange
13: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms)
13: [----------] 4 tests from GaussianOn1DLattice (0 ms total)
13:
13: [----------] 9 tests from GaussTransformTest
13: [ RUN ] GaussTransformTest.isZeroUponConstruction
13: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms)
13: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss
13: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms)
13: [ RUN ] GaussTransformTest.isZeroAfterSettingZero
13: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms)
13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX
13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms)
13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY
13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms)
13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ
13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms)
13: [ RUN ] GaussTransformTest.complementaryGaussAddToZero
13: [ OK ] GaussTransformTest.complementaryGaussAddToZero (1 ms)
13: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues
13: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms)
13: [ RUN ] GaussTransformTest.view
13: [ OK ] GaussTransformTest.view (0 ms)
13: [----------] 9 tests from GaussTransformTest (1 ms total)
13:
13: [----------] 3 tests from DensityFittingForce
13: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity
13: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms)
13: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections
13: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms)
13: [ RUN ] DensityFittingForce.pullsTowardsDerivative
13: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms)
13: [----------] 3 tests from DensityFittingForce (0 ms total)
13:
13: [----------] 2 tests from InvertMatrixTest
13: [ RUN ] InvertMatrixTest.IdentityIsImpotent
13: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
13: [ RUN ] InvertMatrixTest.ComputesInverse
13: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
13: [----------] 2 tests from InvertMatrixTest (0 ms total)
13:
13: [----------] 2 tests from InvertBoxMatrixTest
13: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
13: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
13: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
13: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
13: [----------] 2 tests from InvertBoxMatrixTest (0 ms total)
13:
13: [----------] 15 tests from MatrixTest
13: [ RUN ] MatrixTest.canSetFromArray
13: [ OK ] MatrixTest.canSetFromArray (0 ms)
13: [ RUN ] MatrixTest.canSetStaticallyFromList
13: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms)
13: [ RUN ] MatrixTest.canConstructAndFill
13: [ OK ] MatrixTest.canConstructAndFill (0 ms)
13: [ RUN ] MatrixTest.canSetValues
13: [ OK ] MatrixTest.canSetValues (0 ms)
13: [ RUN ] MatrixTest.canCopyAssign
13: [ OK ] MatrixTest.canCopyAssign (0 ms)
13: [ RUN ] MatrixTest.canSwap
13: [ OK ] MatrixTest.canSwap (0 ms)
13: [ RUN ] MatrixTest.staticMultiDimArrayExtent
13: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms)
13: [ RUN ] MatrixTest.determinantWorks
13: [ OK ] MatrixTest.determinantWorks (0 ms)
13: [ RUN ] MatrixTest.noninvertableDeterminantIsZero
13: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms)
13: [ RUN ] MatrixTest.determinantOfDiagonalMatrix
13: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms)
13: [ RUN ] MatrixTest.traceWorks
13: [ OK ] MatrixTest.traceWorks (0 ms)
13: [ RUN ] MatrixTest.transposeWorks
13: [ OK ] MatrixTest.transposeWorks (0 ms)
13: [ RUN ] MatrixTest.transposeOfSymmetricMatrix
13: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms)
13: [ RUN ] MatrixTest.canCreateFromLegacyMatrix
13: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms)
13: [ RUN ] MatrixTest.canFillLegacyMatrix
13: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms)
13: [----------] 15 tests from MatrixTest (0 ms total)
13:
13: [----------] 25 tests from MultiDimArrayTest
13: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic
13: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic
13: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (1 ms)
13: [ RUN ] MultiDimArrayTest.canSetValuesInStatic
13: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic
13: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveConstructStatic
13: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic
13: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveAssignStatic
13: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic
13: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyConstructStatic
13: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic
13: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyAssignStatic
13: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic
13: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSwapStatic
13: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSwapDynamic
13: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent
13: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms)
13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent
13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms)
13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent
13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms)
13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue
13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms)
13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray
13: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms)
13: [ RUN ] MultiDimArrayTest.conversionToView
13: [ OK ] MultiDimArrayTest.conversionToView (0 ms)
13: [ RUN ] MultiDimArrayTest.conversionToConstView
13: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms)
13: [ RUN ] MultiDimArrayTest.viewBegin
13: [ OK ] MultiDimArrayTest.viewBegin (0 ms)
13: [ RUN ] MultiDimArrayTest.viewEnd
13: [ OK ] MultiDimArrayTest.viewEnd (0 ms)
13: [ RUN ] MultiDimArrayTest.constViewConstBegin
13: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms)
13: [ RUN ] MultiDimArrayTest.constViewConstEnd
13: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms)
13: [----------] 25 tests from MultiDimArrayTest (2 ms total)
13:
13: [----------] 4 tests from MultiDimArrayToMdSpanTest
13: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms)
13: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms)
13: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms)
13: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms)
13: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
13: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/0.CanCopyAssign
13: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/0.CanMoveAssign
13: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/0.CanSwap
13: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/0 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
13: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/1.CanCopyAssign
13: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/1.CanMoveAssign
13: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/1.CanSwap
13: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/1 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
13: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/2.CanCopyAssign
13: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/2.CanMoveAssign
13: [ OK ] PaddedVectorTest/2.CanMoveAssign (1 ms)
13: [ RUN ] PaddedVectorTest/2.CanSwap
13: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/2 (1 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
13: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/3.CanCopyAssign
13: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/3.CanMoveAssign
13: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/3.CanSwap
13: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/3 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
13: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/4.CanCopyAssign
13: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/4.CanMoveAssign
13: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/4.CanSwap
13: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/4 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/5.CanCopyAssign
13: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/5.CanMoveAssign
13: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/5.CanSwap
13: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/5 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/6.CanCopyAssign
13: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/6.CanMoveAssign
13: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/6.CanSwap
13: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/6 (1 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/7.CanCopyAssign
13: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/7.CanMoveAssign
13: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/7.CanSwap
13: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/7 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/8.CanCopyAssign
13: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/8.CanMoveAssign
13: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/8.CanSwap
13: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/8 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/9.CanCopyAssign
13: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/9.CanMoveAssign
13: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/9.CanSwap
13: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/9 (1 ms total)
13:
13: [----------] 37 tests from RVecTest
13: [ RUN ] RVecTest.CanBeStoredInVector
13: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
13: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
13: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
13: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
13: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
13: [ RUN ] RVecTest.WorksAsMutable_rvec
13: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
13: [ RUN ] RVecTest.WorksAs_rvec_Array
13: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
13: [ RUN ] RVecTest.CanAddRVecToRvec
13: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
13: [ RUN ] RVecTest.CanAddAssignRVecToRvec
13: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
13: [ RUN ] RVecTest.CanSubtractRVecFromRvec
13: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
13: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
13: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
13: [ RUN ] RVecTest.CanDotProductRVecByRvec
13: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
13: [ RUN ] RVecTest.CanCrossProductRVecByRvec
13: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
13: [ RUN ] RVecTest.CanDivideRVecInplace
13: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
13: [ RUN ] RVecTest.CanScaleRVec
13: [ OK ] RVecTest.CanScaleRVec (0 ms)
13: [ RUN ] RVecTest.CanDivideRVec
13: [ OK ] RVecTest.CanDivideRVec (0 ms)
13: [ RUN ] RVecTest.CanDoUnitvFromRVec
13: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
13: [ RUN ] RVecTest.CanSqLengthOfRVec
13: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanLengthOfRVec
13: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanCastToRVec
13: [ OK ] RVecTest.CanCastToRVec (0 ms)
13: [ RUN ] RVecTest.CanCastToDVec
13: [ OK ] RVecTest.CanCastToDVec (0 ms)
13: [ RUN ] RVecTest.CanLeftScalarMultiply
13: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
13: [ RUN ] RVecTest.CanRightScalarMultiply
13: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
13: [ RUN ] RVecTest.CanGetUnitvFromRVec
13: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
13: [ RUN ] RVecTest.CanGetSqLengthOfRVec
13: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanGetLengthOfRVec
13: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanDoCrossProductOfRVec
13: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
13: [ RUN ] RVecTest.CanDoDotProductOfRVec
13: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
13: [ RUN ] RVecTest.CanScaleByVector
13: [ OK ] RVecTest.CanScaleByVector (0 ms)
13: [ RUN ] RVecTest.asIVec
13: [ OK ] RVecTest.asIVec (0 ms)
13: [ RUN ] RVecTest.elementWiseMin
13: [ OK ] RVecTest.elementWiseMin (0 ms)
13: [ RUN ] RVecTest.elementWiseMax
13: [ OK ] RVecTest.elementWiseMax (0 ms)
13: [ RUN ] RVecTest.WorksAs_dvec_Reference
13: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
13: [ RUN ] RVecTest.WorksAs_ivec_Reference
13: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
13: [ RUN ] RVecTest.WorksAs_rvec_Reference
13: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
13: [ RUN ] RVecTest.CopyConstructorWorks
13: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
13: [ RUN ] RVecTest.CopyAssignmentWorks
13: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
13: [ RUN ] RVecTest.MoveConstructorWorks
13: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
13: [ RUN ] RVecTest.MoveAssignmentWorks
13: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
13: [----------] 37 tests from RVecTest (1 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 204 tests from 29 test cases ran. (304 ms total)
13: [ PASSED ] 204 tests.
13/54 Test #13: MathUnitTests ....................... Passed 0.34 sec
test 14
Start 14: MdrunUtilityUnitTests
14: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml"
14: Test timeout computed to be: 30
14: [==========] Running 17 tests from 1 test case.
14: [----------] Global test environment set-up.
14: [----------] 17 tests from ThreadAffinityTest
14: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
14: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
14: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
14: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms)
14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
14: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms)
14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
14: NOTE: Affinity setting failed.
14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms)
14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (2 ms)
14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
14: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (1 ms)
14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
14: NOTE: Affinity setting for 1/2 threads failed.
14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (3 ms)
14: [----------] 17 tests from ThreadAffinityTest (15 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 17 tests from 1 test case ran. (15 ms total)
14: [ PASSED ] 17 tests.
14/54 Test #14: MdrunUtilityUnitTests ............... Passed 0.04 sec
test 15
Start 15: MdrunUtilityMpiUnitTests
15: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
15: Test timeout computed to be: 30
15: [==========] Running 13 tests from 2 test cases.
15: [----------] Global test environment set-up.
15: [----------] 6 tests from ThreadAffinityMultiRankTest
15: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
15: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (6 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
15: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (7 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
15: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (5 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
15: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (2 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (3 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (3 ms)
15: [----------] 6 tests from ThreadAffinityMultiRankTest (26 ms total)
15:
15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (5 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (5 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (6 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (5 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (4 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (7 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (5 ms)
15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (38 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 13 tests from 2 test cases ran. (65 ms total)
15: [ PASSED ] 13 tests.
15/54 Test #15: MdrunUtilityMpiUnitTests ............ Passed 0.08 sec
test 16
Start 16: MDSpanTests
16: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MDSpanTests.xml"
16: Test timeout computed to be: 30
16: [==========] Running 32 tests from 7 test cases.
16: [----------] Global test environment set-up.
16: [----------] 4 tests from BasicAccessorPolicy
16: [ RUN ] BasicAccessorPolicy.Decay
16: [ OK ] BasicAccessorPolicy.Decay (0 ms)
16: [ RUN ] BasicAccessorPolicy.Access
16: [ OK ] BasicAccessorPolicy.Access (0 ms)
16: [ RUN ] BasicAccessorPolicy.Offset
16: [ OK ] BasicAccessorPolicy.Offset (0 ms)
16: [ RUN ] BasicAccessorPolicy.CopyAccessor
16: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms)
16: [----------] 4 tests from BasicAccessorPolicy (0 ms total)
16:
16: [----------] 4 tests from ExtentsTest
16: [ RUN ] ExtentsTest.Construction
16: [ OK ] ExtentsTest.Construction (0 ms)
16: [ RUN ] ExtentsTest.PurelyStatic
16: [ OK ] ExtentsTest.PurelyStatic (0 ms)
16: [ RUN ] ExtentsTest.RankNought
16: [ OK ] ExtentsTest.RankNought (0 ms)
16: [ RUN ] ExtentsTest.Assignment
16: [ OK ] ExtentsTest.Assignment (0 ms)
16: [----------] 4 tests from ExtentsTest (0 ms total)
16:
16: [----------] 8 tests from MdSpanExtension
16: [ RUN ] MdSpanExtension.SlicingAllStatic
16: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms)
16: [ RUN ] MdSpanExtension.SlicingDynamic
16: [ OK ] MdSpanExtension.SlicingDynamic (0 ms)
16: [ RUN ] MdSpanExtension.SlicingAllStatic3D
16: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms)
16: [ RUN ] MdSpanExtension.SlicingEqualsView3D
16: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms)
16: [ RUN ] MdSpanExtension.additionWorks
16: [ OK ] MdSpanExtension.additionWorks (0 ms)
16: [ RUN ] MdSpanExtension.subtractionWorks
16: [ OK ] MdSpanExtension.subtractionWorks (0 ms)
16: [ RUN ] MdSpanExtension.multiplicationWorks
16: [ OK ] MdSpanExtension.multiplicationWorks (0 ms)
16: [ RUN ] MdSpanExtension.divisionWorks
16: [ OK ] MdSpanExtension.divisionWorks (0 ms)
16: [----------] 8 tests from MdSpanExtension (1 ms total)
16:
16: [----------] 3 tests from LayoutTests
16: [ RUN ] LayoutTests.LayoutRightConstruction
16: [ OK ] LayoutTests.LayoutRightConstruction (0 ms)
16: [ RUN ] LayoutTests.LayoutRightProperties
16: [ OK ] LayoutTests.LayoutRightProperties (0 ms)
16: [ RUN ] LayoutTests.LayoutRightOperator
16: [ OK ] LayoutTests.LayoutRightOperator (0 ms)
16: [----------] 3 tests from LayoutTests (0 ms total)
16:
16: [----------] 1 test from MdSpanTest
16: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly
16: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms)
16: [----------] 1 test from MdSpanTest (0 ms total)
16:
16: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan<int, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<int> >
16: [ RUN ] MdSpanTest/0.Rank
16: [ OK ] MdSpanTest/0.Rank (0 ms)
16: [ RUN ] MdSpanTest/0.DynamicRank
16: [ OK ] MdSpanTest/0.DynamicRank (0 ms)
16: [ RUN ] MdSpanTest/0.Extents
16: [ OK ] MdSpanTest/0.Extents (0 ms)
16: [ RUN ] MdSpanTest/0.Strides
16: [ OK ] MdSpanTest/0.Strides (0 ms)
16: [ RUN ] MdSpanTest/0.Properties
16: [ OK ] MdSpanTest/0.Properties (0 ms)
16: [ RUN ] MdSpanTest/0.Operator
16: [ OK ] MdSpanTest/0.Operator (0 ms)
16: [----------] 6 tests from MdSpanTest/0 (0 ms total)
16:
16: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan<float, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<float> >
16: [ RUN ] MdSpanTest/1.Rank
16: [ OK ] MdSpanTest/1.Rank (0 ms)
16: [ RUN ] MdSpanTest/1.DynamicRank
16: [ OK ] MdSpanTest/1.DynamicRank (0 ms)
16: [ RUN ] MdSpanTest/1.Extents
16: [ OK ] MdSpanTest/1.Extents (0 ms)
16: [ RUN ] MdSpanTest/1.Strides
16: [ OK ] MdSpanTest/1.Strides (0 ms)
16: [ RUN ] MdSpanTest/1.Properties
16: [ OK ] MdSpanTest/1.Properties (0 ms)
16: [ RUN ] MdSpanTest/1.Operator
16: [ OK ] MdSpanTest/1.Operator (0 ms)
16: [----------] 6 tests from MdSpanTest/1 (1 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 32 tests from 7 test cases ran. (2 ms total)
16: [ PASSED ] 32 tests.
16/54 Test #16: MDSpanTests ......................... Passed 0.02 sec
test 17
Start 17: OnlineHelpUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 22 tests from 4 test cases.
17: [----------] Global test environment set-up.
17: [----------] 6 tests from TextTableFormatterTest
17: [ RUN ] TextTableFormatterTest.HandlesBasicCase
17: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms)
17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
17: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms)
17: [ RUN ] TextTableFormatterTest.HandlesIndentation
17: [ OK ] TextTableFormatterTest.HandlesIndentation (1 ms)
17: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
17: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms)
17: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
17: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms)
17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
17: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms)
17: [----------] 6 tests from TextTableFormatterTest (1 ms total)
17:
17: [----------] 3 tests from HelpManagerTest
17: [ RUN ] HelpManagerTest.HandlesRootTopic
17: [ OK ] HelpManagerTest.HandlesRootTopic (1 ms)
17: [ RUN ] HelpManagerTest.HandlesSubTopics
17: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms)
17: [ RUN ] HelpManagerTest.HandlesInvalidTopics
17: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms)
17: [----------] 3 tests from HelpManagerTest (1 ms total)
17:
17: [----------] 2 tests from HelpTopicFormattingTest
17: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
17: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (1 ms)
17: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
17: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms)
17: [----------] 2 tests from HelpTopicFormattingTest (1 ms total)
17:
17: [----------] 11 tests from HelpWriterContextTest
17: [ RUN ] HelpWriterContextTest.FormatsParagraphs
17: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
17: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms)
17: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
17: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsLiteralText
17: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
17: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
17: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsBulletList
17: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
17: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
17: [ OK ] HelpWriterContextTest.FormatsSimpleTable (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsGridTable
17: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsTitles
17: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms)
17: [----------] 11 tests from HelpWriterContextTest (3 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 22 tests from 4 test cases ran. (6 ms total)
17: [ PASSED ] 22 tests.
17/54 Test #17: OnlineHelpUnitTests ................. Passed 0.03 sec
test 18
Start 18: OptionsUnitTests
18: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 110 tests from 18 test cases.
18: [----------] Global test environment set-up.
18: [----------] 5 tests from AbstractOptionStorageTest
18: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
18: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms)
18: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
18: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms)
18: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
18: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms)
18: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
18: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (1 ms)
18: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
18: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms)
18: [----------] 5 tests from AbstractOptionStorageTest (2 ms total)
18:
18: [----------] 8 tests from FileNameOptionTest
18: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
18: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
18: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
18: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
18: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
18: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
18: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
18: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
18: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms)
18: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
18: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
18: [----------] 8 tests from FileNameOptionTest (1 ms total)
18:
18: [----------] 15 tests from FileNameOptionManagerTest
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
18: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (1 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
18: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
18: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
18: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
18: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms)
18: [----------] 15 tests from FileNameOptionManagerTest (1 ms total)
18:
18: [----------] 1 test from OptionsTest
18: [ RUN ] OptionsTest.FailsOnNonsafeStorage
18: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms)
18: [----------] 1 test from OptionsTest (0 ms total)
18:
18: [----------] 9 tests from OptionsAssignerTest
18: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
18: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
18: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
18: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
18: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesMissingValue
18: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesExtraValue
18: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesGroups
18: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesSections
18: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
18: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
18: [----------] 9 tests from OptionsAssignerTest (0 ms total)
18:
18: [----------] 4 tests from OptionsAssignerBooleanTest
18: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
18: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms)
18: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
18: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
18: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
18: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
18: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
18: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms)
18: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total)
18:
18: [----------] 13 tests from OptionsAssignerIntegerTest
18: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
18: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
18: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
18: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
18: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
18: [ OK ] OptionsAssignerIntegerTest.StoresToVector (1 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
18: [----------] 13 tests from OptionsAssignerIntegerTest (1 ms total)
18:
18: [----------] 5 tests from OptionsAssignerDoubleTest
18: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
18: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
18: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
18: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
18: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
18: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
18: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total)
18:
18: [----------] 9 tests from OptionsAssignerStringTest
18: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
18: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
18: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
18: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
18: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (1 ms)
18: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
18: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
18: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
18: [----------] 9 tests from OptionsAssignerStringTest (1 ms total)
18:
18: [----------] 6 tests from OptionsAssignerEnumTest
18: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
18: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
18: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
18: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
18: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total)
18:
18: [----------] 8 tests from RepeatingOptionSectionTest
18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
18: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
18: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
18: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
18: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms)
18: [----------] 8 tests from RepeatingOptionSectionTest (1 ms total)
18:
18: [----------] 1 test from TimeUnitManagerTest
18: [ RUN ] TimeUnitManagerTest.BasicOperations
18: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
18: [----------] 1 test from TimeUnitManagerTest (0 ms total)
18:
18: [----------] 4 tests from TimeUnitBehaviorTest
18: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
18: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
18: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
18: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
18: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
18: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
18: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
18: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms)
18: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total)
18:
18: [----------] 2 tests from TreeValueSupportAssignTest
18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
18: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms)
18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
18: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
18: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total)
18:
18: [----------] 1 test from TreeValueSupportAssignErrorTest
18: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
18: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms)
18: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total)
18:
18: [----------] 5 tests from TreeValueSupportCheckTest
18: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
18: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
18: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
18: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
18: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total)
18:
18: [----------] 6 tests from TreeValueSupportAdjustTest
18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (1 ms)
18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
18: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
18: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
18: [ OK ] TreeValueSupportAdjustTest.OrdersValues (1 ms)
18: [----------] 6 tests from TreeValueSupportAdjustTest (2 ms total)
18:
18: [----------] 8 tests from TreeValueSupportTest
18: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
18: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
18: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsInt64Option
18: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms)
18: [ RUN ] TreeValueSupportTest.SupportsStringOption
18: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsFloatOption
18: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
18: [ OK ] TreeValueSupportTest.SupportsDoubleOption (1 ms)
18: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption
18: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsEnumOption
18: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms)
18: [----------] 8 tests from TreeValueSupportTest (2 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 110 tests from 18 test cases ran. (14 ms total)
18: [ PASSED ] 110 tests.
18/54 Test #18: OptionsUnitTests .................... Passed 0.04 sec
test 19
Start 19: PbcutilUnitTest
19: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml"
19: Test timeout computed to be: 30
19: [==========] Running 3 tests from 2 test cases.
19: [----------] Global test environment set-up.
19: [----------] 1 test from PbcTest
19: [ RUN ] PbcTest.CalcShiftsWorks
19: [ OK ] PbcTest.CalcShiftsWorks (1 ms)
19: [----------] 1 test from PbcTest (1 ms total)
19:
19: [----------] 2 tests from PbcEnumsTest
19: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect
19: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms)
19: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect
19: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms)
19: [----------] 2 tests from PbcEnumsTest (0 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 3 tests from 2 test cases ran. (1 ms total)
19: [ PASSED ] 3 tests.
19/54 Test #19: PbcutilUnitTest ..................... Passed 0.02 sec
test 20
Start 20: RandomUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/RandomUnitTests.xml"
20: Test timeout computed to be: 30
20: [==========] Running 44 tests from 10 test cases.
20: [----------] Global test environment set-up.
20: [----------] 4 tests from ExponentialDistributionTest
20: [ RUN ] ExponentialDistributionTest.Output
20: [ OK ] ExponentialDistributionTest.Output (0 ms)
20: [ RUN ] ExponentialDistributionTest.Logical
20: [ OK ] ExponentialDistributionTest.Logical (0 ms)
20: [ RUN ] ExponentialDistributionTest.Reset
20: [ OK ] ExponentialDistributionTest.Reset (0 ms)
20: [ RUN ] ExponentialDistributionTest.AltParam
20: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from ExponentialDistributionTest (0 ms total)
20:
20: [----------] 4 tests from GammaDistributionTest
20: [ RUN ] GammaDistributionTest.Output
20: [ OK ] GammaDistributionTest.Output (0 ms)
20: [ RUN ] GammaDistributionTest.Logical
20: [ OK ] GammaDistributionTest.Logical (0 ms)
20: [ RUN ] GammaDistributionTest.Reset
20: [ OK ] GammaDistributionTest.Reset (0 ms)
20: [ RUN ] GammaDistributionTest.AltParam
20: [ OK ] GammaDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from GammaDistributionTest (1 ms total)
20:
20: [----------] 4 tests from NormalDistributionTest
20: [ RUN ] NormalDistributionTest.Output
20: [ OK ] NormalDistributionTest.Output (0 ms)
20: [ RUN ] NormalDistributionTest.Logical
20: [ OK ] NormalDistributionTest.Logical (0 ms)
20: [ RUN ] NormalDistributionTest.Reset
20: [ OK ] NormalDistributionTest.Reset (0 ms)
20: [ RUN ] NormalDistributionTest.AltParam
20: [ OK ] NormalDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from NormalDistributionTest (0 ms total)
20:
20: [----------] 1 test from SeedTest
20: [ RUN ] SeedTest.makeRandomSeed
20: [ OK ] SeedTest.makeRandomSeed (0 ms)
20: [----------] 1 test from SeedTest (0 ms total)
20:
20: [----------] 6 tests from TabulatedNormalDistributionTest
20: [ RUN ] TabulatedNormalDistributionTest.Output14
20: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.Output16
20: [ OK ] TabulatedNormalDistributionTest.Output16 (1 ms)
20: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
20: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.Logical
20: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.Reset
20: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.AltParam
20: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
20: [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total)
20:
20: [----------] 1 test from TabulatedNormalDistributionTableTest
20: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
20: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (3 ms)
20: [----------] 1 test from TabulatedNormalDistributionTableTest (3 ms total)
20:
20: [----------] 6 tests from ThreeFry2x64Test
20: [ RUN ] ThreeFry2x64Test.Logical
20: [ OK ] ThreeFry2x64Test.Logical (0 ms)
20: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
20: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms)
20: [ RUN ] ThreeFry2x64Test.Reseed
20: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
20: [ RUN ] ThreeFry2x64Test.Discard
20: [ OK ] ThreeFry2x64Test.Discard (0 ms)
20: [ RUN ] ThreeFry2x64Test.InvalidCounter
20: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms)
20: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
20: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
20: [----------] 6 tests from ThreeFry2x64Test (0 ms total)
20:
20: [----------] 4 tests from UniformIntDistributionTest
20: [ RUN ] UniformIntDistributionTest.Output
20: [ OK ] UniformIntDistributionTest.Output (0 ms)
20: [ RUN ] UniformIntDistributionTest.Logical
20: [ OK ] UniformIntDistributionTest.Logical (0 ms)
20: [ RUN ] UniformIntDistributionTest.Reset
20: [ OK ] UniformIntDistributionTest.Reset (0 ms)
20: [ RUN ] UniformIntDistributionTest.AltParam
20: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from UniformIntDistributionTest (1 ms total)
20:
20: [----------] 5 tests from UniformRealDistributionTest
20: [ RUN ] UniformRealDistributionTest.GenerateCanonical
20: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms)
20: [ RUN ] UniformRealDistributionTest.Output
20: [ OK ] UniformRealDistributionTest.Output (0 ms)
20: [ RUN ] UniformRealDistributionTest.Logical
20: [ OK ] UniformRealDistributionTest.Logical (0 ms)
20: [ RUN ] UniformRealDistributionTest.Reset
20: [ OK ] UniformRealDistributionTest.Reset (0 ms)
20: [ RUN ] UniformRealDistributionTest.AltParam
20: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
20: [----------] 5 tests from UniformRealDistributionTest (1 ms total)
20:
20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (1 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms)
20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (1 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 44 tests from 10 test cases ran. (9 ms total)
20: [ PASSED ] 44 tests.
20/54 Test #20: RandomUnitTests ..................... Passed 0.04 sec
test 21
Start 21: RestraintTests
21: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/RestraintTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 1 test from 1 test case.
21: [----------] Global test environment set-up.
21: [----------] 1 test from RestraintManager
21: [ RUN ] RestraintManager.restraintList
21: [ OK ] RestraintManager.restraintList (0 ms)
21: [----------] 1 test from RestraintManager (0 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 1 test from 1 test case ran. (0 ms total)
21: [ PASSED ] 1 test.
21/54 Test #21: RestraintTests ...................... Passed 0.02 sec
test 22
Start 22: TableUnitTests
22: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TableUnitTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 16 tests from 2 test cases.
22: [----------] Global test environment set-up.
22: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
22: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
22: [ OK ] SplineTableTest/0.HandlesIncorrectInput (3 ms)
22: [ RUN ] SplineTableTest/0.Sinc
22: [ OK ] SplineTableTest/0.Sinc (1 ms)
22: [ RUN ] SplineTableTest/0.LJ12
22: [ OK ] SplineTableTest/0.LJ12 (28 ms)
22: [ RUN ] SplineTableTest/0.PmeCorrection
22: [ OK ] SplineTableTest/0.PmeCorrection (3 ms)
22: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
22: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (0 ms)
22: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
22: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (2 ms)
22: [ RUN ] SplineTableTest/0.TwoFunctions
22: [ OK ] SplineTableTest/0.TwoFunctions (54 ms)
22: [ RUN ] SplineTableTest/0.ThreeFunctions
22: [ OK ] SplineTableTest/0.ThreeFunctions (63 ms)
22: [----------] 8 tests from SplineTableTest/0 (155 ms total)
22:
22: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
22: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
22: [ OK ] SplineTableTest/1.HandlesIncorrectInput (2 ms)
22: [ RUN ] SplineTableTest/1.Sinc
22: [ OK ] SplineTableTest/1.Sinc (4 ms)
22: [ RUN ] SplineTableTest/1.LJ12
22: [ OK ] SplineTableTest/1.LJ12 (67 ms)
22: [ RUN ] SplineTableTest/1.PmeCorrection
22: [ OK ] SplineTableTest/1.PmeCorrection (3 ms)
22: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
22: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms)
22: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
22: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (2 ms)
22: [ RUN ] SplineTableTest/1.TwoFunctions
22: [ OK ] SplineTableTest/1.TwoFunctions (134 ms)
22: [ RUN ] SplineTableTest/1.ThreeFunctions
22: [ OK ] SplineTableTest/1.ThreeFunctions (154 ms)
22: [----------] 8 tests from SplineTableTest/1 (367 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 16 tests from 2 test cases ran. (522 ms total)
22: [ PASSED ] 16 tests.
22/54 Test #22: TableUnitTests ...................... Passed 0.54 sec
test 23
Start 23: TaskAssignmentUnitTests
23: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 3 tests from 2 test cases.
23: [----------] Global test environment set-up.
23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest
23: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork
23: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (1 ms)
23: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid
23: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (1 ms)
23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (2 ms total)
23:
23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest
23: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow
23: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (1 ms)
23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (1 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 3 tests from 2 test cases ran. (3 ms total)
23: [ PASSED ] 3 tests.
23/54 Test #23: TaskAssignmentUnitTests ............. Passed 0.02 sec
test 24
Start 24: TopologyTest
24: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/topology-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TopologyTest.xml"
24: Test timeout computed to be: 30
24: [==========] Running 11 tests from 3 test cases.
24: [----------] Global test environment set-up.
24: [----------] 3 tests from ExclusionBlockTest
24: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks
24: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms)
24: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka
24: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms)
24: [ RUN ] ExclusionBlockTest.MergeExclusions
24: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms)
24: [----------] 3 tests from ExclusionBlockTest (0 ms total)
24:
24: [----------] 2 tests from MtopTest
24: [ RUN ] MtopTest.RangeBasedLoop
24: [ OK ] MtopTest.RangeBasedLoop (0 ms)
24: [ RUN ] MtopTest.Operators
24: [ OK ] MtopTest.Operators (0 ms)
24: [----------] 2 tests from MtopTest (0 ms total)
24:
24: [----------] 6 tests from SymtabTest
24: [ RUN ] SymtabTest.EmptyOnOpen
24: [ OK ] SymtabTest.EmptyOnOpen (0 ms)
24: [ RUN ] SymtabTest.AddSingleEntry
24: [ OK ] SymtabTest.AddSingleEntry (0 ms)
24: [ RUN ] SymtabTest.AddTwoDistinctEntries
24: [ OK ] SymtabTest.AddTwoDistinctEntries (0 ms)
24: [ RUN ] SymtabTest.TryToAddDuplicates
24: [ OK ] SymtabTest.TryToAddDuplicates (0 ms)
24: [ RUN ] SymtabTest.AddLargeNumberOfEntries
24: [ OK ] SymtabTest.AddLargeNumberOfEntries (0 ms)
24: [ RUN ] SymtabTest.NoDuplicatesInLargeTable
24: [ OK ] SymtabTest.NoDuplicatesInLargeTable (0 ms)
24: [----------] 6 tests from SymtabTest (1 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 11 tests from 3 test cases ran. (1 ms total)
24: [ PASSED ] 11 tests.
24/54 Test #24: TopologyTest ........................ Passed 0.02 sec
test 25
Start 25: PullTest
25: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/PullTest.xml"
25: Test timeout computed to be: 30
25: [==========] Running 5 tests from 1 test case.
25: [----------] Global test environment set-up.
25: [----------] 5 tests from PullTest
25: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
25: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
25: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
25: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
25: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
25: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
25: [----------] 5 tests from PullTest (0 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 5 tests from 1 test case ran. (1 ms total)
25: [ PASSED ] 5 tests.
25/54 Test #25: PullTest ............................ Passed 0.02 sec
test 26
Start 26: AwhTest
26: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AwhTest.xml"
26: Test timeout computed to be: 30
26: [==========] Running 12 tests from 4 test cases.
26: [----------] Global test environment set-up.
26: [----------] 1 test from BiasTest
26: [ RUN ] BiasTest.DetectsCovering
26: [ OK ] BiasTest.DetectsCovering (1 ms)
26: [----------] 1 test from BiasTest (1 ms total)
26:
26: [----------] 1 test from gridTest
26: [ RUN ] gridTest.neighborhood
26: [ OK ] gridTest.neighborhood (2 ms)
26: [----------] 1 test from gridTest (2 ms total)
26:
26: [----------] 8 tests from WithParameters/BiasTest
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (0 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (1 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (1 ms)
26: [----------] 8 tests from WithParameters/BiasTest (7 ms total)
26:
26: [----------] 2 tests from WithParameters/BiasStateTest
26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms)
26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms)
26: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 12 tests from 4 test cases ran. (12 ms total)
26: [ PASSED ] 12 tests.
26/54 Test #26: AwhTest ............................. Passed 0.03 sec
test 27
Start 27: SimdUnitTests
27: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/SimdUnitTests.xml"
27: Test timeout computed to be: 30
27: [==========] Running 86 tests from 3 test cases.
27: [----------] Global test environment set-up.
27: [----------] 41 tests from SimdScalarTest
27: [ RUN ] SimdScalarTest.load
27: [ OK ] SimdScalarTest.load (0 ms)
27: [ RUN ] SimdScalarTest.loadU
27: [ OK ] SimdScalarTest.loadU (0 ms)
27: [ RUN ] SimdScalarTest.store
27: [ OK ] SimdScalarTest.store (0 ms)
27: [ RUN ] SimdScalarTest.storeU
27: [ OK ] SimdScalarTest.storeU (0 ms)
27: [ RUN ] SimdScalarTest.setZero
27: [ OK ] SimdScalarTest.setZero (0 ms)
27: [ RUN ] SimdScalarTest.andNot
27: [ OK ] SimdScalarTest.andNot (0 ms)
27: [ RUN ] SimdScalarTest.fma
27: [ OK ] SimdScalarTest.fma (0 ms)
27: [ RUN ] SimdScalarTest.fms
27: [ OK ] SimdScalarTest.fms (0 ms)
27: [ RUN ] SimdScalarTest.fnma
27: [ OK ] SimdScalarTest.fnma (0 ms)
27: [ RUN ] SimdScalarTest.fnms
27: [ OK ] SimdScalarTest.fnms (0 ms)
27: [ RUN ] SimdScalarTest.maskAdd
27: [ OK ] SimdScalarTest.maskAdd (0 ms)
27: [ RUN ] SimdScalarTest.maskzMul
27: [ OK ] SimdScalarTest.maskzMul (0 ms)
27: [ RUN ] SimdScalarTest.maskzFma
27: [ OK ] SimdScalarTest.maskzFma (0 ms)
27: [ RUN ] SimdScalarTest.abs
27: [ OK ] SimdScalarTest.abs (0 ms)
27: [ RUN ] SimdScalarTest.max
27: [ OK ] SimdScalarTest.max (0 ms)
27: [ RUN ] SimdScalarTest.min
27: [ OK ] SimdScalarTest.min (0 ms)
27: [ RUN ] SimdScalarTest.round
27: [ OK ] SimdScalarTest.round (0 ms)
27: [ RUN ] SimdScalarTest.trunc
27: [ OK ] SimdScalarTest.trunc (0 ms)
27: [ RUN ] SimdScalarTest.reduce
27: [ OK ] SimdScalarTest.reduce (0 ms)
27: [ RUN ] SimdScalarTest.testBits
27: [ OK ] SimdScalarTest.testBits (0 ms)
27: [ RUN ] SimdScalarTest.anyTrue
27: [ OK ] SimdScalarTest.anyTrue (0 ms)
27: [ RUN ] SimdScalarTest.selectByMask
27: [ OK ] SimdScalarTest.selectByMask (0 ms)
27: [ RUN ] SimdScalarTest.selectByNotMask
27: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
27: [ RUN ] SimdScalarTest.blend
27: [ OK ] SimdScalarTest.blend (0 ms)
27: [ RUN ] SimdScalarTest.cvtR2I
27: [ OK ] SimdScalarTest.cvtR2I (0 ms)
27: [ RUN ] SimdScalarTest.cvttR2I
27: [ OK ] SimdScalarTest.cvttR2I (0 ms)
27: [ RUN ] SimdScalarTest.cvtI2R
27: [ OK ] SimdScalarTest.cvtI2R (0 ms)
27: [ RUN ] SimdScalarTest.cvtF2D
27: [ OK ] SimdScalarTest.cvtF2D (0 ms)
27: [ RUN ] SimdScalarTest.cvtD2D
27: [ OK ] SimdScalarTest.cvtD2D (0 ms)
27: [ RUN ] SimdScalarTest.loadI
27: [ OK ] SimdScalarTest.loadI (0 ms)
27: [ RUN ] SimdScalarTest.loadUI
27: [ OK ] SimdScalarTest.loadUI (0 ms)
27: [ RUN ] SimdScalarTest.storeI
27: [ OK ] SimdScalarTest.storeI (0 ms)
27: [ RUN ] SimdScalarTest.storeUI
27: [ OK ] SimdScalarTest.storeUI (0 ms)
27: [ RUN ] SimdScalarTest.andNotI
27: [ OK ] SimdScalarTest.andNotI (0 ms)
27: [ RUN ] SimdScalarTest.testBitsI
27: [ OK ] SimdScalarTest.testBitsI (0 ms)
27: [ RUN ] SimdScalarTest.selectByMaskI
27: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
27: [ RUN ] SimdScalarTest.selectByNotMaskI
27: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
27: [ RUN ] SimdScalarTest.blendI
27: [ OK ] SimdScalarTest.blendI (0 ms)
27: [ RUN ] SimdScalarTest.cvtB2IB
27: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
27: [ RUN ] SimdScalarTest.cvtIB2B
27: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
27: [ RUN ] SimdScalarTest.expandScalarsToTriplets
27: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
27: [----------] 41 tests from SimdScalarTest (3 ms total)
27:
27: [----------] 8 tests from SimdScalarUtilTest
27: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
27: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
27: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
27: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
27: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
27: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
27: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
27: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
27: [----------] 8 tests from SimdScalarUtilTest (0 ms total)
27:
27: [----------] 37 tests from SimdScalarMathTest
27: [ RUN ] SimdScalarMathTest.copysign
27: [ OK ] SimdScalarMathTest.copysign (0 ms)
27: [ RUN ] SimdScalarMathTest.invsqrtPair
27: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
27: [ RUN ] SimdScalarMathTest.inv
27: [ OK ] SimdScalarMathTest.inv (0 ms)
27: [ RUN ] SimdScalarMathTest.maskzInvsqrt
27: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
27: [ RUN ] SimdScalarMathTest.log
27: [ OK ] SimdScalarMathTest.log (0 ms)
27: [ RUN ] SimdScalarMathTest.exp2
27: [ OK ] SimdScalarMathTest.exp2 (0 ms)
27: [ RUN ] SimdScalarMathTest.exp
27: [ OK ] SimdScalarMathTest.exp (0 ms)
27: [ RUN ] SimdScalarMathTest.erf
27: [ OK ] SimdScalarMathTest.erf (0 ms)
27: [ RUN ] SimdScalarMathTest.erfc
27: [ OK ] SimdScalarMathTest.erfc (0 ms)
27: [ RUN ] SimdScalarMathTest.sincos
27: [ OK ] SimdScalarMathTest.sincos (0 ms)
27: [ RUN ] SimdScalarMathTest.sin
27: [ OK ] SimdScalarMathTest.sin (0 ms)
27: [ RUN ] SimdScalarMathTest.cos
27: [ OK ] SimdScalarMathTest.cos (0 ms)
27: [ RUN ] SimdScalarMathTest.tan
27: [ OK ] SimdScalarMathTest.tan (0 ms)
27: [ RUN ] SimdScalarMathTest.asin
27: [ OK ] SimdScalarMathTest.asin (0 ms)
27: [ RUN ] SimdScalarMathTest.acos
27: [ OK ] SimdScalarMathTest.acos (0 ms)
27: [ RUN ] SimdScalarMathTest.atan
27: [ OK ] SimdScalarMathTest.atan (0 ms)
27: [ RUN ] SimdScalarMathTest.atan2
27: [ OK ] SimdScalarMathTest.atan2 (0 ms)
27: [ RUN ] SimdScalarMathTest.pmeForceCorrection
27: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
27: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
27: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
27: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
27: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.invSingleAccuracy
27: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
27: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.logSingleAccuracy
27: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
27: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.expSingleAccuracy
27: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
27: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
27: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
27: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
27: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
27: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
27: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
27: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
27: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
27: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
27: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
27: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
27: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
27: [----------] 37 tests from SimdScalarMathTest (3 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 86 tests from 3 test cases ran. (6 ms total)
27: [ PASSED ] 86 tests.
27/54 Test #27: SimdUnitTests ....................... Passed 0.03 sec
test 28
Start 28: CompatibilityHelpersTests
28: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml"
28: Test timeout computed to be: 30
28: [==========] Running 170 tests from 12 test cases.
28: [----------] Global test environment set-up.
28: [----------] 45 tests from OptionalTest
28: [ RUN ] OptionalTest.UnionCanContainNonPodTypes
28: [ OK ] OptionalTest.UnionCanContainNonPodTypes (0 ms)
28: [ RUN ] OptionalTest.CanDefaultConstructEmpty
28: [ OK ] OptionalTest.CanDefaultConstructEmpty (0 ms)
28: [ RUN ] OptionalTest.CanConstructFromNullopt
28: [ OK ] OptionalTest.CanConstructFromNullopt (0 ms)
28: [ RUN ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType
28: [ OK ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptional
28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptional
28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion
28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptional
28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting
28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptional
28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromLiteral
28: [ OK ] OptionalTest.CanCopyConstructFromLiteral (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromLiteralConverting
28: [ OK ] OptionalTest.CanCopyConstructFromLiteralConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromValue
28: [ OK ] OptionalTest.CanCopyConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromValueConverting
28: [ OK ] OptionalTest.CanCopyConstructFromValueConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromValue
28: [ OK ] OptionalTest.CanMoveConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromValueExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromValueExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceConstructFromLiteral
28: [ OK ] OptionalTest.CanInPlaceConstructFromLiteral (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromValue
28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromValue
28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromInitializerList
28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromInitializerList (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromInitializerList
28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromInitializerList (0 ms)
28: [ RUN ] OptionalTest.CanAssignNulloptToDisengage
28: [ OK ] OptionalTest.CanAssignNulloptToDisengage (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals
28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting
28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting
28: [ OK ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignFromLiteral
28: [ OK ] OptionalTest.CanCopyAssignFromLiteral (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignFromValue
28: [ OK ] OptionalTest.CanCopyAssignFromValue (0 ms)
28: [ RUN ] OptionalTest.CanMoveAssignFromValue
28: [ OK ] OptionalTest.CanMoveAssignFromValue (0 ms)
28: [ RUN ] OptionalTest.CanCopyEmplaceFromArguments
28: [ OK ] OptionalTest.CanCopyEmplaceFromArguments (0 ms)
28: [ RUN ] OptionalTest.CanMoveEmplaceFromArguments
28: [ OK ] OptionalTest.CanMoveEmplaceFromArguments (1 ms)
28: [ RUN ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments
28: [ OK ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments (0 ms)
28: [ RUN ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments
28: [ OK ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments (0 ms)
28: [ RUN ] OptionalTest.CanResetContent
28: [ OK ] OptionalTest.CanResetContent (0 ms)
28: [ RUN ] OptionalTest.ProvidesRelationalOperators
28: [ OK ] OptionalTest.ProvidesRelationalOperators (0 ms)
28: [ RUN ] OptionalTest.ProvidesMixedTypeRelationalOperators
28: [ OK ] OptionalTest.ProvidesMixedTypeRelationalOperators (1 ms)
28: [ RUN ] OptionalTest.CanProduceHash
28: [ OK ] OptionalTest.CanProduceHash (0 ms)
28: [ RUN ] OptionalTest.ShowAlignmentDependingOnBaseType
28: alignment_of<char>: 1
28: alignment_of<short>: 2
28: alignment_of<int>: 4
28: alignment_of<long>: 4
28: alignment_of<float>: 4
28: alignment_of<double>: 8
28: alignment_of<long double>: 8
28: alignment_of<Struct>: 1
28: [ OK ] OptionalTest.ShowAlignmentDependingOnBaseType (0 ms)
28: [ RUN ] OptionalTest.ShowSizeDependingOnBaseType
28: sizeof( nonstd::optional_lite::detail::storage_t<char> ): 1
28: sizeof( optional<char> ): 2 (1)
28: sizeof( optional<short> ): 4 (2)
28: sizeof( optional<int> ): 8 (4)
28: sizeof( optional<long> ): 8 (4)
28: sizeof( optional<float> ): 8 (4)
28: sizeof( optional<double> ): 16 (8)
28: sizeof( optional<long double> ): 16 (8)
28: sizeof( optional<Struct> ): 2 (1)
28: [ OK ] OptionalTest.ShowSizeDependingOnBaseType (0 ms)
28: [----------] 45 tests from OptionalTest (4 ms total)
28:
28: [----------] 7 tests from MakeOptionalTest
28: [ RUN ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals
28: [ OK ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals (0 ms)
28: [ RUN ] MakeOptionalTest.CanCopyConstruct
28: [ OK ] MakeOptionalTest.CanCopyConstruct (0 ms)
28: [ RUN ] MakeOptionalTest.CanMoveConstruct
28: [ OK ] MakeOptionalTest.CanMoveConstruct (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments
28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments
28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments
28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments
28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments (0 ms)
28: [----------] 7 tests from MakeOptionalTest (1 ms total)
28:
28: [----------] 4 tests from OptionalMemberSwapTest
28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged
28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged (0 ms)
28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged
28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged (0 ms)
28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged
28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged (0 ms)
28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged
28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged (0 ms)
28: [----------] 4 tests from OptionalMemberSwapTest (0 ms total)
28:
28: [----------] 4 tests from OptionalImplicitValueTest
28: [ RUN ] OptionalImplicitValueTest.CanObtainValueConst
28: [ OK ] OptionalImplicitValueTest.CanObtainValueConst (0 ms)
28: [ RUN ] OptionalImplicitValueTest.CanObtainValueNonConst
28: [ OK ] OptionalImplicitValueTest.CanObtainValueNonConst (0 ms)
28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueConst
28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueConst (0 ms)
28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst
28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst (0 ms)
28: [----------] 4 tests from OptionalImplicitValueTest (0 ms total)
28:
28: [----------] 20 tests from OptionalIntValueTest
28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst
28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst
28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool
28: [ OK ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodConst
28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst
28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues
28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues (0 ms)
28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues
28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues (0 ms)
28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod
28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged (0 ms)
28: [----------] 20 tests from OptionalIntValueTest (2 ms total)
28:
28: [----------] 1 test from NotNullConstruction
28: [ RUN ] NotNullConstruction.Works
28: [ OK ] NotNullConstruction.Works (0 ms)
28: [----------] 1 test from NotNullConstruction (0 ms total)
28:
28: [----------] 1 test from NotNullCasting
28: [ RUN ] NotNullCasting.Works
28: [ OK ] NotNullCasting.Works (0 ms)
28: [----------] 1 test from NotNullCasting (0 ms total)
28:
28: [----------] 1 test from NotNullAssignment
28: [ RUN ] NotNullAssignment.Works
28: [ OK ] NotNullAssignment.Works (0 ms)
28: [----------] 1 test from NotNullAssignment (0 ms total)
28:
28: [----------] 1 test from MakeNotNull
28: [ RUN ] MakeNotNull.Works
28: [ OK ] MakeNotNull.Works (0 ms)
28: [----------] 1 test from MakeNotNull (0 ms total)
28:
28: [----------] 1 test from NotNull
28: [ RUN ] NotNull.WorksInContainers
28: [ OK ] NotNull.WorksInContainers (0 ms)
28: [----------] 1 test from NotNull (0 ms total)
28:
28: [----------] 80 tests from StringViewTest
28: [ RUN ] StringViewTest.CanDefaultConstructEmptyView
28: [ OK ] StringViewTest.CanDefaultConstructEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanConstructFromPointerAndSize
28: [ OK ] StringViewTest.CanConstructFromPointerAndSize (0 ms)
28: [ RUN ] StringViewTest.CanConstructFromCString
28: [ OK ] StringViewTest.CanConstructFromCString (0 ms)
28: [ RUN ] StringViewTest.CanCopyConstructFromEmptyView
28: [ OK ] StringViewTest.CanCopyConstructFromEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanCopyConstructFromNonEmptyView
28: [ OK ] StringViewTest.CanCopyConstructFromNonEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanCopyAssingFromEmptyView
28: [ OK ] StringViewTest.CanCopyAssingFromEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanCopyAssingFromNonEmptyView
28: [ OK ] StringViewTest.CanCopyAssingFromNonEmptyView (1 ms)
28: [ RUN ] StringViewTest.AllowForwardIteration
28: [ OK ] StringViewTest.AllowForwardIteration (0 ms)
28: [ RUN ] StringViewTest.AllowConstForwardIteration
28: [ OK ] StringViewTest.AllowConstForwardIteration (0 ms)
28: [ RUN ] StringViewTest.AllowReverseIteration
28: [ OK ] StringViewTest.AllowReverseIteration (0 ms)
28: [ RUN ] StringViewTest.AllowConstReverseIteration
28: [ OK ] StringViewTest.AllowConstReverseIteration (0 ms)
28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaSize
28: [ OK ] StringViewTest.CanObtainSizeFromViewViaSize (0 ms)
28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaLength
28: [ OK ] StringViewTest.CanObtainSizeFromViewViaLength (0 ms)
28: [ RUN ] StringViewTest.CanObtainMaxSizeViaMaxSize
28: [ OK ] StringViewTest.CanObtainMaxSizeViaMaxSize (0 ms)
28: [ RUN ] StringViewTest.CanCheckForEmptyStringWithEmpty
28: [ OK ] StringViewTest.CanCheckForEmptyStringWithEmpty (0 ms)
28: [ RUN ] StringViewTest.CanAccessElementViaArrayIndex
28: [ OK ] StringViewTest.CanAccessElementViaArrayIndex (0 ms)
28: [ RUN ] StringViewTest.CanAccessElementViaAt
28: [ OK ] StringViewTest.CanAccessElementViaAt (0 ms)
28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsAccess
28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsAccess (0 ms)
28: [ RUN ] StringViewTest.CanAccessAllElementsViaData
28: [ OK ] StringViewTest.CanAccessAllElementsViaData (0 ms)
28: [ RUN ] StringViewTest.DataFromEmptyStringIsNullptr
28: [ OK ] StringViewTest.DataFromEmptyStringIsNullptr (0 ms)
28: [ RUN ] StringViewTest.CanRemovePrefix
28: [ OK ] StringViewTest.CanRemovePrefix (0 ms)
28: [ RUN ] StringViewTest.CanRemoveSuffix
28: [ OK ] StringViewTest.CanRemoveSuffix (0 ms)
28: [ RUN ] StringViewTest.CanSwapWithOtherView
28: [ OK ] StringViewTest.CanSwapWithOtherView (0 ms)
28: [ RUN ] StringViewTest.CanCopySubstringWithCopy
28: [ OK ] StringViewTest.CanCopySubstringWithCopy (0 ms)
28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsCopy
28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsCopy (0 ms)
28: [ RUN ] StringViewTest.CanObtainSubstringWithSubstr
28: [ OK ] StringViewTest.CanObtainSubstringWithSubstr (0 ms)
28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsSubstr
28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsSubstr (0 ms)
28: [ RUN ] StringViewTest.CanLexicallyCompareViewWithCompare
28: [ OK ] StringViewTest.CanLexicallyCompareViewWithCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareEmptyViewsWIthCompare
28: [ OK ] StringViewTest.CanCompareEmptyViewsWIthCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringWithViewViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringWithViewViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareToCStringViaCompare
28: [ OK ] StringViewTest.CanCompareToCStringViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringToCStringViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringToCStringViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCheckForPrefixViewViaStartsWith
28: [ OK ] StringViewTest.CanCheckForPrefixViewViaStartsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith
28: [ OK ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForPrefixCStringViaStartsWith
28: [ OK ] StringViewTest.CanCheckForPrefixCStringViaStartsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForSuffixViewViaEndsWith
28: [ OK ] StringViewTest.CanCheckForSuffixViewViaEndsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith
28: [ OK ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForSuffixCStringViaEndsWith
28: [ OK ] StringViewTest.CanCheckForSuffixCStringViaEndsWith (0 ms)
28: [ RUN ] StringViewTest.CanSearchForViewSubstrViaFind
28: [ OK ] StringViewTest.CanSearchForViewSubstrViaFind (1 ms)
28: [ RUN ] StringViewTest.CanSearchForCharacterViaFind
28: [ OK ] StringViewTest.CanSearchForCharacterViaFind (0 ms)
28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFind
28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFind (0 ms)
28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos
28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind
28: [ OK ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForCharacterViaFind
28: [ OK ] StringViewTest.CanBackwardsSearchForCharacterViaFind (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind
28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos
28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharacter
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharacter (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNotFoundCharacter
28: [ OK ] StringViewTest.CanSearchForFirstNotFoundCharacter (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNonMatchingCharacter
28: [ OK ] StringViewTest.CanSearchForFirstNonMatchingCharacter (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength
28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString
28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView
28: [ OK ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter
28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength
28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString
28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSV
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSV (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SV
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SV (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCompareToViews
28: [ OK ] StringViewTest.CanCompareToViews (0 ms)
28: [ RUN ] StringViewTest.CanCompareViewToImplicitlyConvertedView
28: [ OK ] StringViewTest.CanCompareViewToImplicitlyConvertedView (0 ms)
28: [ RUN ] StringViewTest.EmptyViewsCompareAsEqual
28: [ OK ] StringViewTest.EmptyViewsCompareAsEqual (0 ms)
28: [ RUN ] StringViewTest.CanPrintViewToPutputStream
28: [ OK ] StringViewTest.CanPrintViewToPutputStream (0 ms)
28: [ RUN ] StringViewTest.HashOfViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfViewIsEqualToHashOfString (0 ms)
28: [ RUN ] StringViewTest.HashOfWStringViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfWStringViewIsEqualToHashOfString (0 ms)
28: [ RUN ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString (0 ms)
28: [ RUN ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString (0 ms)
28: [----------] 80 tests from StringViewTest (5 ms total)
28:
28: [----------] 5 tests from StringViewExtensionTest
28: [ RUN ] StringViewExtensionTest.CanConstructViewFromString
28: [ OK ] StringViewExtensionTest.CanConstructViewFromString (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToString
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToString (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView (0 ms)
28: [----------] 5 tests from StringViewExtensionTest (0 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 170 tests from 12 test cases ran. (12 ms total)
28: [ PASSED ] 170 tests.
28/54 Test #28: CompatibilityHelpersTests ........... Passed 0.04 sec
test 29
Start 29: GmxAnaTest
29: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxAnaTest.xml"
29: Test timeout computed to be: 600
29: [==========] Running 27 tests from 5 test cases.
29: [----------] Global test environment set-up.
29: [----------] 5 tests from Entropy
29: [ RUN ] Entropy.Schlitter_300_NoLinear
29: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms)
29: [ RUN ] Entropy.Schlitter_300_Linear
29: [ OK ] Entropy.Schlitter_300_Linear (1 ms)
29: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
29: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms)
29: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
29: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms)
29: [ RUN ] Entropy.QuasiHarmonic_200_Linear
29: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms)
29: [----------] 5 tests from Entropy (1 ms total)
29:
29: [----------] 10 tests from MindistTest
29: [ RUN ] MindistTest.mindistWorksWithSingleAtoms
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.mindistWorksWithSingleAtoms (3 ms)
29: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 2: 'atom3'
29: Selected 3: 'atoms12'
29: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (3 ms)
29: [ RUN ] MindistTest.mindistDoesNotPickUpContacts
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.mindistDoesNotPickUpContacts (2 ms)
29: [ RUN ] MindistTest.mindistPicksUpContacts
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.mindistPicksUpContacts (3 ms)
29: [ RUN ] MindistTest.ngWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: Selected 2: 'atom3'
29: [ OK ] MindistTest.ngWorks (2 ms)
29: [ RUN ] MindistTest.groupWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 3: 'atoms12'
29: Selected 2: 'atom3'
29: [ OK ] MindistTest.groupWorks (2 ms)
29: [ RUN ] MindistTest.maxDistWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 2: 'atom3'
29: Selected 3: 'atoms12'
29: [ OK ] MindistTest.maxDistWorks (3 ms)
29: [ RUN ] MindistTest.noPbcWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.noPbcWorks (2 ms)
29: [ RUN ] MindistTest.resPerTimeWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 3: 'atoms12'
29: Selected 2: 'atom3'
29: [ OK ] MindistTest.resPerTimeWorks (3 ms)
29: [ RUN ] MindistTest.matrixWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 5: 'atoms123'
29: Special case: making distance matrix between all atoms in group atoms123
29: [ OK ] MindistTest.matrixWorks (2 ms)
29: [----------] 10 tests from MindistTest (26 ms total)
29:
29: [----------] 3 tests from MsdTest
29: [ RUN ] MsdTest.threeDimensionalDiffusion
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( particles) has 3 elements
29: There is one group in the index
29:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
29:
29: Used 1 restart points spaced 200 ps over 9 ps
29:
29: Fitting from 1 to 8 ps
29:
29: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
29: [ OK ] MsdTest.threeDimensionalDiffusion (3 ms)
29: [ RUN ] MsdTest.twoDimensionalDiffusion
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( particles) has 3 elements
29: There is one group in the index
29:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
29:
29: Used 1 restart points spaced 200 ps over 9 ps
29:
29: Fitting from 1 to 8 ps
29:
29: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
29: [ OK ] MsdTest.twoDimensionalDiffusion (2 ms)
29: [ RUN ] MsdTest.oneDimensionalDiffusion
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( particles) has 3 elements
29: There is one group in the index
29:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
29:
29: Used 1 restart points spaced 200 ps over 9 ps
29:
29: Fitting from 1 to 8 ps
29:
29: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
29: [ OK ] MsdTest.oneDimensionalDiffusion (3 ms)
29: [----------] 3 tests from MsdTest (8 ms total)
29:
29: [----------] 3 tests from MsdMolTest
29: [ RUN ] MsdMolTest.diffMolMassWeighted
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
29: For a correct single-point energy evaluation with nsteps = 0, use
29: continuation = yes to avoid constraining the input coordinates.
29:
29: Setting the LD random seed to 281062358
29: Generated 330891 of the 330891 non-bonded parameter combinations
29: Generating 1-4 interactions: fudge = 0.5
29: Generated 330891 of the 330891 1-4 parameter combinations
29: Excluding 2 bonded neighbours molecule type 'SOL'
29: Number of degrees of freedom in T-Coupling group rest is 27.00
29:
29: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
29: NVE simulation with an initial temperature of zero: will use a Verlet
29: buffer of 10%. Check your energy drift!
29:
29:
29: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
29: You are using a plain Coulomb cut-off, which might produce artifacts.
29: You might want to consider using PME electrostatics.
29:
29:
29:
29: There were 3 notes
29: Calculating diffusion coefficients for molecules.
29: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
29: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( water) has 15 elements
29: There is one group in the index
29: Split group of 15 atoms into 5 molecules
29: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
29:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
29:
29: Used 1 restart points spaced 200 ps over 0.1 ps
29:
29: This run will generate roughly 0 Mb of data
29: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
29: Fitting from 0.008 to 0.088 ps
29:
29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
29: [ OK ] MsdMolTest.diffMolMassWeighted (1086 ms)
29: [ RUN ] MsdMolTest.diffMolNonMassWeighted
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
29: For a correct single-point energy evaluation with nsteps = 0, use
29: continuation = yes to avoid constraining the input coordinates.
29:
29: Setting the LD random seed to -2125416939
29: Generated 330891 of the 330891 non-bonded parameter combinations
29: Generating 1-4 interactions: fudge = 0.5
29: Generated 330891 of the 330891 1-4 parameter combinations
29: Excluding 2 bonded neighbours molecule type 'SOL'
29: Number of degrees of freedom in T-Coupling group rest is 27.00
29:
29: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
29: NVE simulation with an initial temperature of zero: will use a Verlet
29: buffer of 10%. Check your energy drift!
29:
29:
29: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
29: You are using a plain Coulomb cut-off, which might produce artifacts.
29: You might want to consider using PME electrostatics.
29:
29:
29:
29: There were 3 notes
29: Calculating diffusion coefficients for molecules.
29: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
29: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( water) has 15 elements
29: There is one group in the index
29: Split group of 15 atoms into 5 molecules
29: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
29:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
29:
29: Used 1 restart points spaced 200 ps over 0.1 ps
29:
29: This run will generate roughly 0 Mb of data
29: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
29: Fitting from 0.008 to 0.088 ps
29:
29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
29: [ OK ] MsdMolTest.diffMolNonMassWeighted (1076 ms)
29: [ RUN ] MsdMolTest.diffMolSelected
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
29: For a correct single-point energy evaluation with nsteps = 0, use
29: continuation = yes to avoid constraining the input coordinates.
29:
29: Setting the LD random seed to -1404094495
29: Generated 330891 of the 330891 non-bonded parameter combinations
29: Generating 1-4 interactions: fudge = 0.5
29: Generated 330891 of the 330891 1-4 parameter combinations
29: Excluding 2 bonded neighbours molecule type 'SOL'
29: Number of degrees of freedom in T-Coupling group rest is 27.00
29:
29: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
29: NVE simulation with an initial temperature of zero: will use a Verlet
29: buffer of 10%. Check your energy drift!
29:
29:
29: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
29: You are using a plain Coulomb cut-off, which might produce artifacts.
29: You might want to consider using PME electrostatics.
29:
29:
29:
29: There were 3 notes
29: Calculating diffusion coefficients for molecules.
29: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
29: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( mol) has 9 elements
29: There is one group in the index
29: Split group of 9 atoms into 3 molecules
29: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
29:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
29:
29: Used 1 restart points spaced 200 ps over 0.1 ps
29:
29: This run will generate roughly 0 Mb of data
29: <D> = 7.3593 Std. Dev. = 9.7910 Error = 5.6529
29: Fitting from 0.008 to 0.088 ps
29:
29: D[ mol] 7.8614 (+/- 1.5619) 1e-5 cm^2/s
29: [ OK ] MsdMolTest.diffMolSelected (1075 ms)
29: [----------] 3 tests from MsdMolTest (3237 ms total)
29:
29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group: trr version: GMX_trn_file (single precision)
29:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (3 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (5 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (3 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group: Reading frames from gro file '', 6 atoms.
29:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (4 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
29:
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (3 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (4 ms)
29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (23 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 27 tests from 5 test cases ran. (3295 ms total)
29: [ PASSED ] 27 tests.
29/54 Test #29: GmxAnaTest .......................... Passed 3.32 sec
test 30
Start 30: GmxPreprocessTests
30: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml"
30: Test timeout computed to be: 30
30: [==========] Running 51 tests from 9 test cases.
30: [----------] Global test environment set-up.
30: [----------] 4 tests from GenconfTest
30: [ RUN ] GenconfTest.nbox_Works
30: [ OK ] GenconfTest.nbox_Works (1 ms)
30: [ RUN ] GenconfTest.nbox_norenumber_Works
30: [ OK ] GenconfTest.nbox_norenumber_Works (1 ms)
30: [ RUN ] GenconfTest.nbox_dist_Works
30: [ OK ] GenconfTest.nbox_dist_Works (2 ms)
30: [ RUN ] GenconfTest.nbox_rot_Works
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: [ OK ] GenconfTest.nbox_rot_Works (2 ms)
30: [----------] 4 tests from GenconfTest (7 ms total)
30:
30: [----------] 2 tests from GenionTest
30: [ RUN ] GenionTest.HighConcentrationIonPlacement
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
30: buffer. The cluster pair list does have a buffering effect, but choosing
30: a larger rlist might be necessary for good energy conservation.
30:
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to -421197537
30: Generated 331705 of the 331705 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 331705 of the 331705 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Excluding 3 bonded neighbours molecule type 'methane'
30: Number of degrees of freedom in T-Coupling group rest is 1308.00
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
30: Group 0 ( System) has 653 elements
30: Group 1 ( Water) has 648 elements
30: Group 2 ( SOL) has 648 elements
30: Group 3 ( non-Water) has 5 elements
30: Group 4 ( Other) has 5 elements
30: Group 5 ( METH) has 5 elements
30: Select a group: Number of (3-atomic) solvent molecules: 216
30: Using random seed 1997.
30: Replacing solvent molecule 56 (atom 168) with NA
30: Replacing solvent molecule 120 (atom 360) with NA
30: Replacing solvent molecule 182 (atom 546) with NA
30: Replacing solvent molecule 71 (atom 213) with NA
30: Replacing solvent molecule 189 (atom 567) with CL
30: Replacing solvent molecule 54 (atom 162) with CL
30: Replacing solvent molecule 155 (atom 465) with CL
30: Replacing solvent molecule 99 (atom 297) with CL
30:
30: Analysing residue names:
30: There are: 216 Water residues
30: There are: 1 Other residues
30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
30: This run will generate roughly 0 Mb of data
30: Will try to add 4 NA ions and 4 CL ions.
30: Select a continuous group of solvent molecules
30: Selected 1: 'Water'
30: [ OK ] GenionTest.HighConcentrationIonPlacement (1066 ms)
30: [ RUN ] GenionTest.NoIonPlacement
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
30: buffer. The cluster pair list does have a buffering effect, but choosing
30: a larger rlist might be necessary for good energy conservation.
30:
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to -1902794275
30: Generated 331705 of the 331705 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 331705 of the 331705 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Excluding 3 bonded neighbours molecule type 'methane'
30: Number of degrees of freedom in T-Coupling group rest is 1308.00
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
30: No ions to add, will just copy input configuration.
30: Analysing residue names:
30: There are: 216 Water residues
30: There are: 1 Other residues
30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
30: This run will generate roughly 0 Mb of data
30: [ OK ] GenionTest.NoIonPlacement (1057 ms)
30: [----------] 2 tests from GenionTest (2123 ms total)
30:
30: [----------] 1 test from GenRestrTest
30: [ RUN ] GenRestrTest.SimpleRestraintsGenerated
30:
30: Reading structure file
30: Group 0 ( System) has 156 elements
30: Group 1 ( Protein) has 156 elements
30: Group 2 ( Protein-H) has 75 elements
30: Group 3 ( C-alpha) has 10 elements
30: Group 4 ( Backbone) has 30 elements
30: Group 5 ( MainChain) has 40 elements
30: Group 6 ( MainChain+Cb) has 49 elements
30: Group 7 ( MainChain+H) has 52 elements
30: Group 8 ( SideChain) has 104 elements
30: Group 9 ( SideChain-H) has 35 elements
30: Select a group: Select group to position restrain
30: Selected 3: 'C-alpha'
30: [ OK ] GenRestrTest.SimpleRestraintsGenerated (5 ms)
30: [----------] 1 test from GenRestrTest (6 ms total)
30:
30: [----------] 9 tests from PreprocessingAtomTypesTest
30: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate
30: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid
30: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks
30: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks
30: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry
30: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound
30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound
30: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber
30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber
30: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms)
30: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total)
30:
30: [----------] 10 tests from PreprocessingBondAtomTypeTest
30: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate
30: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid
30: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks
30: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks
30: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry
30: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType
30: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound
30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound
30: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber
30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber
30: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms)
30: [----------] 10 tests from PreprocessingBondAtomTypeTest (1 ms total)
30:
30: [----------] 5 tests from InsertMoleculesTest
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
30: Reading solute configuration
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 8 atoms)!
30:
30: Added 1 molecules (out of 1 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
30:
30: Output configuration contains 8 atoms in 4 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (4 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 2 atoms)!
30:
Try 2 success (now 4 atoms)!
30:
Try 3 success (now 6 atoms)!
30:
Try 4 success (now 8 atoms)!
30:
Try 5 success (now 10 atoms)!
30:
30: Added 5 molecules (out of 5 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
30:
30: Output configuration contains 10 atoms in 10 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (4 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
30: Reading solute configuration
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 8 atoms)!
30:
Try 2 success (now 10 atoms)!
30:
30: Added 2 molecules (out of 2 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
30:
30: Output configuration contains 10 atoms in 4 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (4 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
30: Reading solute configuration
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 650 atoms)!
30:
Try 2 success (now 652 atoms)!
30:
Try 3 success (now 654 atoms)!
30:
Try 4 success (now 656 atoms)!
30:
30: Added 4 molecules (out of 4 requested)
30: Replaced 8 residues (24 atoms)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
30:
30: Output configuration contains 632 atoms in 212 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (19 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
30:
30:
Try 1 success (now 2 atoms)!
30:
Try 2 success (now 4 atoms)!
30:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
30:
Try 13 success (now 6 atoms)!
30:
30: Added 3 molecules (out of 4 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
30:
30: Output configuration contains 6 atoms in 3 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (5 ms)
30: [----------] 5 tests from InsertMoleculesTest (36 ms total)
30:
30: [----------] 14 tests from GetIrTest
30: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
30: Ignoring obsolete mdp entry 'title'
30: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (11 ms)
30: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals
30: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (9 ms)
30: [ RUN ] GetIrTest.AcceptsKeyWithoutValue
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsKeyWithoutValue (7 ms)
30: [ RUN ] GetIrTest.RejectsValueWithoutKey
30: [ OK ] GetIrTest.RejectsValueWithoutKey (9 ms)
30: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue
30: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (9 ms)
30: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (7 ms)
30: [ RUN ] GetIrTest.AcceptsEmptyLines
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsEmptyLines (7 ms)
30: [ RUN ] GetIrTest.AcceptsElectricField
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsElectricField (6 ms)
30: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (7 ms)
30: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (7 ms)
30: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys
30: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (3 ms)
30: [ RUN ] GetIrTest.AcceptsImplicitSolventNo
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsImplicitSolventNo (7 ms)
30: [ RUN ] GetIrTest.RejectsImplicitSolventYes
30: [ OK ] GetIrTest.RejectsImplicitSolventYes (9 ms)
30: [ RUN ] GetIrTest.AcceptsMimic
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsMimic (7 ms)
30: [----------] 14 tests from GetIrTest (105 ms total)
30:
30: [----------] 5 tests from SolvateTest
30: [ RUN ] SolvateTest.cs_box_Works
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 1x1x1 boxes
30: Solvent box contains 270 atoms in 90 residues
30: Removed 129 solvent atoms due to solvent-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 47 residues
30: Generated solvent containing 141 atoms in 47 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
30:
30: Output configuration contains 141 atoms in 47 residues
30: Volume : 1.331 (nm^3)
30: Density : 1056.36 (g/l)
30: Number of solvent molecules: 47
30:
30: [ OK ] SolvateTest.cs_box_Works (19 ms)
30: [ RUN ] SolvateTest.cs_cp_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 2x2x2 boxes
30: Solvent box contains 3660 atoms in 1220 residues
30: Removed 987 solvent atoms due to solvent-solvent overlap
30: Removed 15 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 886 residues
30: Generated solvent containing 2658 atoms in 886 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
30:
30: Output configuration contains 2664 atoms in 888 residues
30: Volume : 27.2709 (nm^3)
30: Density : 974.777 (g/l)
30: Number of solvent molecules: 886
30:
30: [ OK ] SolvateTest.cs_cp_Works (97 ms)
30: [ RUN ] SolvateTest.cs_cp_p_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 2x2x2 boxes
30: Solvent box contains 3660 atoms in 1220 residues
30: Removed 987 solvent atoms due to solvent-solvent overlap
30: Removed 15 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 886 residues
30: Generated solvent containing 2658 atoms in 886 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
30:
30: Output configuration contains 2664 atoms in 888 residues
30: Volume : 27.2709 (nm^3)
30: Density : 974.777 (g/l)
30: Number of solvent molecules: 886
30:
30: Processing topology
30: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top)
30: [ OK ] SolvateTest.cs_cp_p_Works (98 ms)
30: [ RUN ] SolvateTest.shell_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 2x2x2 boxes
30: Solvent box contains 3660 atoms in 1220 residues
30: Removed 987 solvent atoms due to solvent-solvent overlap
30: Removed 1902 solvent atoms more than 1.000000 nm from solute.
30: Removed 15 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 252 residues
30: Generated solvent containing 756 atoms in 252 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
30:
30: Output configuration contains 762 atoms in 254 residues
30: Volume : 27.2709 (nm^3)
30: Density : 279.3 (g/l)
30: Number of solvent molecules: 252
30:
30: [ OK ] SolvateTest.shell_Works (47 ms)
30: [ RUN ] SolvateTest.update_Topology_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 3x3x3 boxes
30: Solvent box contains 14952 atoms in 4984 residues
30: Removed 2787 solvent atoms due to solvent-solvent overlap
30: Removed 30 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 2 different molecule types:
30: HOH ( 3 atoms): 1876 residues
30: SOL ( 3 atoms): 2169 residues
30: Generated solvent containing 0 atoms in 0 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
30:
30: Output configuration contains 12141 atoms in 4047 residues
30: Volume : 125 (nm^3)
30: Density : 968.963 (g/l)
30: Number of solvent molecules: 4045
30:
30: Processing topology
30: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
30: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
30: [ OK ] SolvateTest.update_Topology_Works (390 ms)
30: [----------] 5 tests from SolvateTest (651 ms total)
30:
30: [----------] 1 test from TopDirTests
30: [ RUN ] TopDirTests.NamesArrayHasCorrectSize
30: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms)
30: [----------] 1 test from TopDirTests (0 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 51 tests from 9 test cases ran. (2930 ms total)
30: [ PASSED ] 51 tests.
30/54 Test #30: GmxPreprocessTests .................. Passed 2.95 sec
test 31
Start 31: Pdb2gmx1Test
31: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml"
31: Test timeout computed to be: 30
31: [==========] Running 24 tests from 1 test case.
31: [----------] Global test environment set-up.
31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 0 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (179 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 0 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (198 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 0 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (182 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 0 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (165 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Marked 124 virtual sites
31: Added 16 dummy masses
31: Added 26 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 130 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (192 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Marked 132 virtual sites
31: Added 10 dummy masses
31: Added 19 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 133 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (210 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Marked 123 virtual sites
31: Added 22 dummy masses
31: Added 35 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 132 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (201 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Marked 111 virtual sites
31: Added 18 dummy masses
31: Added 31 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 116 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (179 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 0 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (178 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 0 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (199 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 0 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (181 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 0 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (165 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Marked 124 virtual sites
31: Added 16 dummy masses
31: Added 26 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 130 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (191 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Marked 132 virtual sites
31: Added 10 dummy masses
31: Added 19 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 133 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (210 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Marked 123 virtual sites
31: Added 22 dummy masses
31: Added 35 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 132 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (199 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Marked 111 virtual sites
31: Added 18 dummy masses
31: Added 31 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 116 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (179 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 0 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (177 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 0 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (198 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 0 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (180 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 0 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (166 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Marked 124 virtual sites
31: Added 16 dummy masses
31: Added 26 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 130 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (190 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Marked 132 virtual sites
31: Added 10 dummy masses
31: Added 19 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 133 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (210 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Marked 123 virtual sites
31: Added 22 dummy masses
31: Added 35 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 132 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (199 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Marked 111 virtual sites
31: Added 18 dummy masses
31: Added 31 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 116 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (180 ms)
31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (4509 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 24 tests from 1 test case ran. (4509 ms total)
31: [ PASSED ] 24 tests.
31/54 Test #31: Pdb2gmx1Test ........................ Passed 4.53 sec
test 32
Start 32: Pdb2gmx2Test
32: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml"
32: Test timeout computed to be: 30
32: [==========] Running 32 tests from 2 test cases.
32: [----------] Global test environment set-up.
32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (129 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (145 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (128 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (120 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Marked 37 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 37 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (130 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Marked 53 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 51 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (149 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Marked 36 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 36 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (132 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Marked 33 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 31 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (125 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (126 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (143 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (128 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (120 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Marked 37 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 37 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (131 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Marked 53 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 51 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (148 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Marked 36 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 36 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (133 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Marked 33 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 31 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (125 ms)
32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (2114 ms total)
32:
32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (137 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (156 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (140 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (133 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Marked 39 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 39 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (143 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Marked 57 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 55 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (161 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Marked 38 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 38 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (145 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Marked 35 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 33 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (137 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (138 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (156 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (139 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (132 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Marked 39 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 39 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (143 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Marked 57 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 55 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (162 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Marked 38 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 38 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (145 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Marked 35 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 33 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (137 ms)
32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (2306 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 32 tests from 2 test cases ran. (4420 ms total)
32: [ PASSED ] 32 tests.
32/54 Test #32: Pdb2gmx2Test ........................ Passed 4.44 sec
test 33
Start 33: Pdb2gmx3Test
33: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml"
33: Test timeout computed to be: 30
33: [==========] Running 28 tests from 4 test cases.
33: [----------] Global test environment set-up.
33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 255, now 254
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 691 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 691 dihedrals, 51 impropers, 457 angles
33: 650 pairs, 254 bonds and 0 virtual sites
33: Total mass 1846.132 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (175 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 291, now 290
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 788 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 788 dihedrals, 72 impropers, 516 angles
33: 736 pairs, 290 bonds and 0 virtual sites
33: Total mass 2088.366 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (192 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 262, now 261
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 727 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 727 dihedrals, 56 impropers, 472 angles
33: 667 pairs, 261 bonds and 0 virtual sites
33: Total mass 1861.124 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (175 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 233, now 232
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 634 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 634 dihedrals, 48 impropers, 419 angles
33: 597 pairs, 232 bonds and 0 virtual sites
33: Total mass 1662.888 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (158 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 255, now 254
33: Marked 124 virtual sites
33: Added 16 dummy masses
33: Added 26 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 691 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 691 dihedrals, 51 impropers, 457 angles
33: 650 pairs, 254 bonds and 130 virtual sites
33: Total mass 1846.132 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (185 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 291, now 290
33: Marked 132 virtual sites
33: Added 10 dummy masses
33: Added 19 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 788 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 788 dihedrals, 72 impropers, 516 angles
33: 736 pairs, 290 bonds and 133 virtual sites
33: Total mass 2088.366 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (204 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 262, now 261
33: Marked 123 virtual sites
33: Added 22 dummy masses
33: Added 35 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 727 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 727 dihedrals, 56 impropers, 472 angles
33: 667 pairs, 261 bonds and 132 virtual sites
33: Total mass 1861.124 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (192 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33:
33: WARNING: Duplicate line found in or between hackblock and rtp entries
33:
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 233, now 232
33: Marked 111 virtual sites
33: Added 18 dummy masses
33: Added 31 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 634 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 634 dihedrals, 48 impropers, 419 angles
33: 597 pairs, 232 bonds and 116 virtual sites
33: Total mass 1662.888 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (171 ms)
33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (1452 ms total)
33:
33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 254, now 254
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 663 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 663 dihedrals, 48 impropers, 457 angles
33: 650 pairs, 254 bonds and 0 virtual sites
33: Total mass 1846.115 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (163 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 290, now 290
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 778 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 778 dihedrals, 49 impropers, 516 angles
33: 736 pairs, 290 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (183 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 261, now 261
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 696 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 696 dihedrals, 39 impropers, 472 angles
33: 667 pairs, 261 bonds and 0 virtual sites
33: Total mass 1861.130 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (165 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 232, now 232
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 618 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 618 dihedrals, 38 impropers, 419 angles
33: 597 pairs, 232 bonds and 0 virtual sites
33: Total mass 1662.885 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (150 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 254, now 254
33: Marked 124 virtual sites
33: Added 16 dummy masses
33: Added 26 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 663 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 663 dihedrals, 48 impropers, 457 angles
33: 650 pairs, 254 bonds and 130 virtual sites
33: Total mass 1846.115 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (177 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 290, now 290
33: Marked 132 virtual sites
33: Added 10 dummy masses
33: Added 19 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 778 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 778 dihedrals, 49 impropers, 516 angles
33: 736 pairs, 290 bonds and 133 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (194 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 261, now 261
33: Marked 123 virtual sites
33: Added 22 dummy masses
33: Added 35 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 696 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 696 dihedrals, 39 impropers, 472 angles
33: 667 pairs, 261 bonds and 132 virtual sites
33: Total mass 1861.130 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (181 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 232, now 232
33: Marked 111 virtual sites
33: Added 18 dummy masses
33: Added 31 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 618 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 618 dihedrals, 38 impropers, 419 angles
33: 597 pairs, 232 bonds and 116 virtual sites
33: Total mass 1662.885 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (164 ms)
33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (1379 ms total)
33:
33: [----------] 8 tests from ChainSep/Pdb2gmxTest
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 258, now 258
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 651 pairs
33: Before cleaning: 661 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 10 cmap torsion pairs
33: There are 661 dihedrals, 46 impropers, 463 angles
33: 648 pairs, 258 bonds and 0 virtual sites
33: Total mass 1882.146 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on changing chain id only (ignoring TER records).
33:
33: Merged chains into joint molecule definitions at 2 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Identified residue PHE6 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Start terminus PHE-6: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 258 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (166 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 50, now 50
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 123 pairs
33: Before cleaning: 123 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 2 cmap torsion pairs
33: There are 123 dihedrals, 9 impropers, 88 angles
33: 123 pairs, 50 bonds and 0 virtual sites
33: Total mass 434.421 a.m.u.
33: Total charge -2.000 e
33: Writing topology
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 10 donors and 7 acceptors were found.
33: There are 7 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS8
33: NE223
33: MET12 SD55 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 125, now 125
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 317 pairs
33: Before cleaning: 322 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 5 cmap torsion pairs
33: There are 322 dihedrals, 19 impropers, 227 angles
33: 314 pairs, 125 bonds and 0 virtual sites
33: Total mass 846.083 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 258 atoms and 16 residues
33: Total mass in system 1882.146 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on changing chain id only (ignoring TER records).
33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 4 28
33: 2 'B' 7 58
33: 3 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (28 atoms, 4 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 4 residues with 51 atoms
33: Chain time...
33: Processing chain 2 'B' (58 atoms, 7 residues)
33: Identified residue PHE6 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus PHE-6: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 7 residues with 124 atoms
33: Chain time...
33: Processing chain 3 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 51 atoms 4 residues
33: Including chain 2 in system: 124 atoms 7 residues
33: Including chain 3 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (123 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 258, now 258
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 651 pairs
33: Before cleaning: 661 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 10 cmap torsion pairs
33: There are 661 dihedrals, 46 impropers, 463 angles
33: 648 pairs, 258 bonds and 0 virtual sites
33: Total mass 1882.146 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records only (ignoring chain id).
33:
33: Merged chains into joint molecule definitions at 2 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ILE-9: COO-
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 258 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (166 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 10 donors and 12 acceptors were found.
33: There are 13 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3
33: SG9
33: HIS8 NE251 1.055
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 115, now 115
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 288 pairs
33: Before cleaning: 293 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 6 cmap torsion pairs
33: There are 293 dihedrals, 23 impropers, 203 angles
33: 285 pairs, 115 bonds and 0 virtual sites
33: Total mass 888.952 a.m.u.
33: Total charge -2.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 60, now 60
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 152 pairs
33: Before cleaning: 152 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 152 dihedrals, 5 impropers, 112 angles
33: 152 pairs, 60 bonds and 0 virtual sites
33: Total mass 391.552 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 258 atoms and 16 residues
33: Total mass in system 1882.146 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records only (ignoring chain id).
33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 8 61
33: 2 'B' 3 25
33: 3 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (61 atoms, 8 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ILE-9: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 8 residues with 114 atoms
33: Chain time...
33: Processing chain 2 'B' (25 atoms, 3 residues)
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 61 atoms
33: Chain time...
33: Processing chain 3 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 114 atoms 8 residues
33: Including chain 2 in system: 61 atoms 3 residues
33: Including chain 3 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (123 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 260, now 260
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 650 pairs
33: Before cleaning: 660 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 8 cmap torsion pairs
33: There are 660 dihedrals, 45 impropers, 466 angles
33: 647 pairs, 260 bonds and 0 virtual sites
33: Total mass 1900.162 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33:
33: Merged chains into joint molecule definitions at 3 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Identified residue PHE6 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Start terminus PHE-6: NH3+
33: End terminus ILE-9: COO-
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 261 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (167 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 50, now 50
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 123 pairs
33: Before cleaning: 123 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 2 cmap torsion pairs
33: There are 123 dihedrals, 9 impropers, 88 angles
33: 123 pairs, 50 bonds and 0 virtual sites
33: Total mass 434.421 a.m.u.
33: Total charge -2.000 e
33: Writing topology
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 6 donors and 4 acceptors were found.
33: There are 3 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 67, now 67
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 164 pairs
33: Before cleaning: 169 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 2 cmap torsion pairs
33: There are 169 dihedrals, 13 impropers, 118 angles
33: 161 pairs, 67 bonds and 0 virtual sites
33: Total mass 472.547 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 60, now 60
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 152 pairs
33: Before cleaning: 152 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 152 dihedrals, 5 impropers, 112 angles
33: 152 pairs, 60 bonds and 0 virtual sites
33: Total mass 391.552 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 261 atoms and 16 residues
33: Total mass in system 1900.162 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: WARNING: Chain identifier 'B' is used in two non-sequential blocks.
33: They will be treated as separate chains unless you reorder your file.
33: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 4 28
33: 2 'B' 4 33
33: 3 'B' 3 25
33: 4 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (28 atoms, 4 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 4 residues with 51 atoms
33: Chain time...
33: Processing chain 2 'B' (33 atoms, 4 residues)
33: Identified residue PHE6 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Start terminus PHE-6: NH3+
33: End terminus ILE-9: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 4 residues with 66 atoms
33: Chain time...
33: Processing chain 3 'B' (25 atoms, 3 residues)
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 61 atoms
33: Chain time...
33: Processing chain 4 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 51 atoms 4 residues
33: Including chain 2 in system: 66 atoms 4 residues
33: Including chain 3 in system: 61 atoms 3 residues
33: Including chain 4 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (123 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 256, now 256
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 652 pairs
33: Before cleaning: 662 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 12 cmap torsion pairs
33: There are 662 dihedrals, 47 impropers, 460 angles
33: 649 pairs, 256 bonds and 0 virtual sites
33: Total mass 1864.131 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records and chain id changing.
33:
33: Merged chains into joint molecule definitions at 1 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (163 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 14 donors and 15 acceptors were found.
33: There are 20 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 173, now 173
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 441 pairs
33: Before cleaning: 446 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 9 cmap torsion pairs
33: There are 446 dihedrals, 29 impropers, 312 angles
33: 438 pairs, 173 bonds and 0 virtual sites
33: Total mass 1262.488 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 255 atoms and 16 residues
33: Total mass in system 1864.131 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records and chain id changing.
33: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 11 86
33: 2 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (86 atoms, 11 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 11 residues with 172 atoms
33: Chain time...
33: Processing chain 2 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 172 atoms 11 residues
33: Including chain 2 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (127 ms)
33: [----------] 8 tests from ChainSep/Pdb2gmxTest (1159 ms total)
33:
33: [----------] 4 tests from ChainChanges/Pdb2gmxTest
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on changing chain id only (ignoring TER records).
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (83 ms)
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records only (ignoring chain id).
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (83 ms)
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (84 ms)
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records and chain id changing.
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (83 ms)
33: [----------] 4 tests from ChainChanges/Pdb2gmxTest (333 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 28 tests from 4 test cases ran. (4323 ms total)
33: [ PASSED ] 28 tests.
33/54 Test #33: Pdb2gmx3Test ........................ Passed 4.35 sec
test 34
Start 34: CorrelationsTest
34: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CorrelationsTest.xml"
34: Test timeout computed to be: 30
34: [==========] Running 21 tests from 3 test cases.
34: [----------] Global test environment set-up.
34: [----------] 10 tests from AutocorrTest
34: [ RUN ] AutocorrTest.EacNormal
34: [ OK ] AutocorrTest.EacNormal (13 ms)
34: [ RUN ] AutocorrTest.EacNoNormalize
34: [ OK ] AutocorrTest.EacNoNormalize (8 ms)
34: [ RUN ] AutocorrTest.EacCos
34: [ OK ] AutocorrTest.EacCos (14 ms)
34: [ RUN ] AutocorrTest.EacVector
34: [ OK ] AutocorrTest.EacVector (19 ms)
34: [ RUN ] AutocorrTest.EacRcross
34: [ OK ] AutocorrTest.EacRcross (3 ms)
34: [ RUN ] AutocorrTest.EacP0
34: [ OK ] AutocorrTest.EacP0 (19 ms)
34: [ RUN ] AutocorrTest.EacP1
34: [ OK ] AutocorrTest.EacP1 (18 ms)
34: [ RUN ] AutocorrTest.EacP2
34: [ OK ] AutocorrTest.EacP2 (35 ms)
34: [ RUN ] AutocorrTest.EacP3
34: [ OK ] AutocorrTest.EacP3 (9 ms)
34: [ RUN ] AutocorrTest.EacP4
34: [ OK ] AutocorrTest.EacP4 (19 ms)
34: [----------] 10 tests from AutocorrTest (166 ms total)
34:
34: [----------] 1 test from ManyAutocorrelationTest
34: [ RUN ] ManyAutocorrelationTest.Empty
34: [ OK ] ManyAutocorrelationTest.Empty (0 ms)
34: [----------] 1 test from ManyAutocorrelationTest (0 ms total)
34:
34: [----------] 10 tests from ExpfitTest
34: [ RUN ] ExpfitTest.EffnEXP1
34: [ OK ] ExpfitTest.EffnEXP1 (1 ms)
34: [ RUN ] ExpfitTest.EffnEXP2
34: [ OK ] ExpfitTest.EffnEXP2 (2 ms)
34: [ RUN ] ExpfitTest.EffnEXPEXP
34: [ OK ] ExpfitTest.EffnEXPEXP (5 ms)
34: [ RUN ] ExpfitTest.EffnEXP5
34: [ OK ] ExpfitTest.EffnEXP5 (13 ms)
34: [ RUN ] ExpfitTest.EffnEXP7
34: [ OK ] ExpfitTest.EffnEXP7 (11 ms)
34: [ RUN ] ExpfitTest.EffnEXP9
34: [ OK ] ExpfitTest.EffnEXP9 (42 ms)
34: [ RUN ] ExpfitTest.EffnERF
34: [ OK ] ExpfitTest.EffnERF (8 ms)
34: [ RUN ] ExpfitTest.EffnERREST
34: [ OK ] ExpfitTest.EffnERREST (2 ms)
34: [ RUN ] ExpfitTest.EffnVAC
34: [ OK ] ExpfitTest.EffnVAC (16 ms)
34: [ RUN ] ExpfitTest.EffnPRES
34: [ OK ] ExpfitTest.EffnPRES (39 ms)
34: [----------] 10 tests from ExpfitTest (141 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 21 tests from 3 test cases ran. (339 ms total)
34: [ PASSED ] 21 tests.
34/54 Test #34: CorrelationsTest .................... Passed 0.36 sec
test 35
Start 35: AnalysisDataUnitTests
35: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml"
35: Test timeout computed to be: 30
35: [==========] Running 69 tests from 14 test cases.
35: [----------] Global test environment set-up.
35: [----------] 3 tests from AnalysisDataInitializationTest
35: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
35: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms)
35: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
35: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms)
35: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
35: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms)
35: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (3 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (5 ms)
35: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (2 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (2 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/0 (26 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
35: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (2 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (3 ms)
35: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (2 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/1 (30 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (6 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (7 ms)
35: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (3 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (2 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/2 (36 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (6 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (5 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (8 ms)
35: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (3 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (3 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/3 (36 ms total)
35:
35: [----------] 4 tests from AnalysisArrayDataTest
35: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
35: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisArrayDataTest.StorageWorks
35: [ OK ] AnalysisArrayDataTest.StorageWorks (2 ms)
35: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
35: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms)
35: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
35: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
35: [----------] 4 tests from AnalysisArrayDataTest (7 ms total)
35:
35: [----------] 6 tests from AverageModuleTest
35: [ RUN ] AverageModuleTest.BasicTest
35: [ OK ] AverageModuleTest.BasicTest (4 ms)
35: [ RUN ] AverageModuleTest.HandlesMultipointData
35: [ OK ] AverageModuleTest.HandlesMultipointData (4 ms)
35: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
35: [ OK ] AverageModuleTest.HandlesMultipleDataSets (5 ms)
35: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
35: [ OK ] AverageModuleTest.HandlesDataSetAveraging (5 ms)
35: [ RUN ] AverageModuleTest.CanCustomizeXAxis
35: [ OK ] AverageModuleTest.CanCustomizeXAxis (4 ms)
35: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
35: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (4 ms)
35: [----------] 6 tests from AverageModuleTest (27 ms total)
35:
35: [----------] 2 tests from FrameAverageModuleTest
35: [ RUN ] FrameAverageModuleTest.BasicTest
35: [ OK ] FrameAverageModuleTest.BasicTest (4 ms)
35: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
35: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (5 ms)
35: [----------] 2 tests from FrameAverageModuleTest (10 ms total)
35:
35: [----------] 7 tests from AnalysisHistogramSettingsTest
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
35: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total)
35:
35: [----------] 2 tests from SimpleHistogramModuleTest
35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (6 ms)
35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (7 ms)
35: [----------] 2 tests from SimpleHistogramModuleTest (13 ms total)
35:
35: [----------] 3 tests from WeightedHistogramModuleTest
35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (6 ms)
35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (6 ms)
35: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
35: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (7 ms)
35: [----------] 3 tests from WeightedHistogramModuleTest (20 ms total)
35:
35: [----------] 3 tests from BinAverageModuleTest
35: [ RUN ] BinAverageModuleTest.ComputesCorrectly
35: [ OK ] BinAverageModuleTest.ComputesCorrectly (5 ms)
35: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
35: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (6 ms)
35: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
35: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (5 ms)
35: [----------] 3 tests from BinAverageModuleTest (16 ms total)
35:
35: [----------] 4 tests from AbstractAverageHistogramTest
35: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
35: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (11 ms)
35: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
35: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (6 ms)
35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (6 ms)
35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (6 ms)
35: [----------] 4 tests from AbstractAverageHistogramTest (31 ms total)
35:
35: [----------] 3 tests from LifetimeModuleTest
35: [ RUN ] LifetimeModuleTest.BasicTest
35: [ OK ] LifetimeModuleTest.BasicTest (4 ms)
35: [ RUN ] LifetimeModuleTest.CumulativeTest
35: [ OK ] LifetimeModuleTest.CumulativeTest (4 ms)
35: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
35: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (4 ms)
35: [----------] 3 tests from LifetimeModuleTest (13 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 69 tests from 14 test cases ran. (265 ms total)
35: [ PASSED ] 69 tests.
35/54 Test #35: AnalysisDataUnitTests ............... Passed 0.29 sec
test 36
Start 36: CoordinateIOTests
36: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml"
36: Test timeout computed to be: 30
36: [==========] Running 64 tests from 19 test cases.
36: [----------] Global test environment set-up.
36: [----------] 1 test from OutputSelectorDeathTest
36: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (12 ms)
36: [----------] 1 test from OutputSelectorDeathTest (12 ms total)
36:
36: [----------] 5 tests from TrajectoryFrameWriterTest
36: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (9 ms)
36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (8 ms)
36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (8 ms)
36: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (17 ms)
36: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks
36: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms)
36: [----------] 5 tests from TrajectoryFrameWriterTest (43 ms total)
36:
36: [----------] 5 tests from OutputAdapterContainer
36: [ RUN ] OutputAdapterContainer.MakeEmpty
36: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms)
36: [ RUN ] OutputAdapterContainer.AddAdapter
36: [ OK ] OutputAdapterContainer.AddAdapter (0 ms)
36: [ RUN ] OutputAdapterContainer.RejectBadAdapter
36: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms)
36: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter
36: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms)
36: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters
36: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms)
36: [----------] 5 tests from OutputAdapterContainer (0 ms total)
36:
36: [----------] 5 tests from FlagTest
36: [ RUN ] FlagTest.CanSetSimpleFlag
36: [ OK ] FlagTest.CanSetSimpleFlag (0 ms)
36: [ RUN ] FlagTest.CanAddNewBox
36: [ OK ] FlagTest.CanAddNewBox (0 ms)
36: [ RUN ] FlagTest.SetsImplicitPrecisionChange
36: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms)
36: [ RUN ] FlagTest.SetsImplicitStartTimeChange
36: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms)
36: [ RUN ] FlagTest.SetsImplicitTimeStepChange
36: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms)
36: [----------] 5 tests from FlagTest (0 ms total)
36:
36: [----------] 5 tests from SetAtomsTest
36: [ RUN ] SetAtomsTest.RemovesExistingAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.RemovesExistingAtoms (9 ms)
36: [ RUN ] SetAtomsTest.AddsNewAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.AddsNewAtoms (8 ms)
36: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (9 ms)
36: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (8 ms)
36: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (9 ms)
36: [----------] 5 tests from SetAtomsTest (43 ms total)
36:
36: [----------] 2 tests from SetBothTimeTest
36: [ RUN ] SetBothTimeTest.StartTimeZeroWorks
36: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms)
36: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks
36: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms)
36: [----------] 2 tests from SetBothTimeTest (0 ms total)
36:
36: [----------] 2 tests from SetStartTimeTest
36: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart
36: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms)
36: [ RUN ] SetStartTimeTest.WorksWithZeroStart
36: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms)
36: [----------] 2 tests from SetStartTimeTest (0 ms total)
36:
36: [----------] 1 test from SetTimeStepTest
36: [ RUN ] SetTimeStepTest.SetTimeStepWorks
36: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms)
36: [----------] 1 test from SetTimeStepTest (0 ms total)
36:
36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (9 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (8 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (9 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (8 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (9 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (8 ms)
36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (51 ms total)
36:
36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles
36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (9 ms)
36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (8 ms)
36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (9 ms)
36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (26 ms total)
36:
36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms)
36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (0 ms total)
36:
36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (18 ms)
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (18 ms)
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (17 ms)
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (18 ms)
36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (71 ms total)
36:
36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles
36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (9 ms)
36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (8 ms)
36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (8 ms)
36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (25 ms total)
36:
36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (1 ms)
36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms)
36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (1 ms total)
36:
36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles
36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (8 ms)
36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (9 ms)
36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (17 ms total)
36:
36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms)
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms)
36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (0 ms total)
36:
36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles
36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (9 ms)
36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (8 ms)
36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (17 ms total)
36:
36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms)
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms)
36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (1 ms total)
36:
36: [----------] 4 tests from ModuleSupported/NoOptionalOutput
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (8 ms)
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (9 ms)
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (8 ms)
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (9 ms)
36: [----------] 4 tests from ModuleSupported/NoOptionalOutput (34 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 64 tests from 19 test cases ran. (342 ms total)
36: [ PASSED ] 64 tests.
36/54 Test #36: CoordinateIOTests ................... Passed 0.37 sec
test 37
Start 37: TrajectoryAnalysisUnitTests
37: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
37: Test timeout computed to be: 30
37: [==========] Running 80 tests from 16 test cases.
37: [----------] Global test environment set-up.
37: [----------] 5 tests from ClustsizeTest
37: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
37: There is one group in the index
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 24
37: cmid: 2, cmax: 4, max_size: 6
37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (5 ms)
37: [ RUN ] ClustsizeTest.NoMolShortCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
37: There is one group in the index
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 24
37: cmid: 1, cmax: 6, max_size: 6
37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (5 ms)
37: [ RUN ] ClustsizeTest.MolDefaultCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 8
37: cmid: 2, cmax: 4, max_size: 2
37: 50%100%cmid: 2, cmax: 6, max_size: 2
37: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (12 ms)
37: [ RUN ] ClustsizeTest.MolShortCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 8
37: cmid: 1, cmax: 6, max_size: 2
37: 50%100%cmid: 2, cmax: 6, max_size: 2
37: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (12 ms)
37: [ RUN ] ClustsizeTest.MolCSize
37: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 8
37: cmid: 2, cmax: 4, max_size: 2
37: 50%100%cmid: 2, cmax: 6, max_size: 2
37: 50%100%[ OK ] ClustsizeTest.MolCSize (12 ms)
37: [----------] 5 tests from ClustsizeTest (47 ms total)
37:
37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (2 ms)
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
37: Reading frames from gro file 'Test system', 8 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (7 ms)
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
37: Reading frames from gro file 'Test system', 8 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (7 ms)
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms)
37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (18 ms total)
37:
37: [----------] 11 tests from AngleModuleTest
37: [ RUN ] AngleModuleTest.ComputesSimpleAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesSimpleAngles (10 ms)
37: [ RUN ] AngleModuleTest.ComputesDihedrals
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesDihedrals (10 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorPairAngles (12 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (12 ms)
37: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (10 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (11 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
37: Reading frames from gro file 'Test system for different angles', 33 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (11 ms)
37: [ RUN ] AngleModuleTest.ComputesMultipleAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesMultipleAngles (15 ms)
37: [ RUN ] AngleModuleTest.HandlesDynamicSelections
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.HandlesDynamicSelections (11 ms)
37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (11 ms)
37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (13 ms)
37: [----------] 11 tests from AngleModuleTest (127 ms total)
37:
37: [----------] 4 tests from ConvertTrjModuleTest
37: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (125 ms)
37: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (127 ms)
37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (10 ms)
37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (11 ms)
37: [----------] 4 tests from ConvertTrjModuleTest (273 ms total)
37:
37: [----------] 3 tests from DistanceModuleTest
37: [ RUN ] DistanceModuleTest.ComputesDistances
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: atomname S1 S2:
37: Number of samples: 5
37: Average distance: 1.43246 nm
37: Standard deviation: 0.96700 nm
37: [ OK ] DistanceModuleTest.ComputesDistances (13 ms)
37: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: atomname S1 S2:
37: Number of samples: 5
37: Average distance: 1.43246 nm
37: Standard deviation: 0.96700 nm
37: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
37: Number of samples: 4
37: Average distance: 1.81066 nm
37: Standard deviation: 0.79289 nm
37: [ OK ] DistanceModuleTest.ComputesMultipleDistances (18 ms)
37: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: atomname S1 S2 and res_cog x < 2.8:
37: Number of samples: 3
37: Average distance: 1.72076 nm
37: Standard deviation: 1.24839 nm
37: [ OK ] DistanceModuleTest.HandlesDynamicSelections (15 ms)
37: [----------] 3 tests from DistanceModuleTest (46 ms total)
37:
37: [----------] 2 tests from ExtractClusterModuleTest
37: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms
37: trr version: GMX_trn_file (single precision)
37:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
37: Analyzed 26 frames, last time 0.050
37: There are 8 clusters containing 26 structures, highest framenr is 25
37: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (11 ms)
37: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset
37:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
37: Analyzed 26 frames, last time 0.050
37: There are 8 clusters containing 26 structures, highest framenr is 25
37: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (11 ms)
37: [----------] 2 tests from ExtractClusterModuleTest (24 ms total)
37:
37: [----------] 2 tests from FreeVolumeModuleTest
37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for 40 particles. These were set to zero.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: cutoff = 0.18 nm
37: probe_radius = 0 nm
37: seed = 13
37: ninsert = 1000 probes per nm^3
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
37: van der Spoel and Luciano T. Costa
37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
37: -------- -------- --- Thank You --- -------- --------
37:
37: Free volume 38.02 +/- 0.00 %
37: Total volume 68.92 +/- 0.00 nm^3
37: Number of molecules 340 total mass 63491.38 Dalton
37: Average molar mass: 186.74 Dalton
37: Density rho: 1529.71 +/- 0.00 nm^3
37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
37: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
37: Fractional free volume 0.194 +/- 0.000
37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (756 ms)
37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: cutoff = 0.18 nm
37: probe_radius = 0 nm
37: seed = 17
37: ninsert = 1000 probes per nm^3
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
37: van der Spoel and Luciano T. Costa
37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
37: -------- -------- --- Thank You --- -------- --------
37:
37: Free volume 38.48 +/- 0.00 %
37: Total volume 68.92 +/- 0.00 nm^3
37: Number of molecules 340 total mass 63491.38 Dalton
37: Average molar mass: 186.74 Dalton
37: Density rho: 1529.71 +/- 0.00 nm^3
37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
37: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
37: Fractional free volume 0.200 +/- 0.000
37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (755 ms)
37: [----------] 2 tests from FreeVolumeModuleTest (1511 ms total)
37:
37: [----------] 7 tests from PairDistanceModuleTest
37: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesAllDistances (9 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (8 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (8 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (8 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (9 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (9 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (9 ms)
37: [----------] 7 tests from PairDistanceModuleTest (64 ms total)
37:
37: [----------] 5 tests from RdfModuleTest
37: [ RUN ] RdfModuleTest.BasicTest
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.BasicTest (63 ms)
37: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
37: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (44 ms)
37: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (63 ms)
37: [ RUN ] RdfModuleTest.CalculatesSurf
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.CalculatesSurf (43 ms)
37: [ RUN ] RdfModuleTest.CalculatesXY
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.CalculatesXY (71 ms)
37: [----------] 5 tests from RdfModuleTest (285 ms total)
37:
37: [----------] 5 tests from SasaModuleTest
37: [ RUN ] SasaModuleTest.BasicTest
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.BasicTest (33 ms)
37: [ RUN ] SasaModuleTest.HandlesSelectedResidues
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.HandlesSelectedResidues (20 ms)
37: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (17 ms)
37: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (27 ms)
37: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (26 ms)
37: [----------] 5 tests from SasaModuleTest (127 ms total)
37:
37: [----------] 8 tests from SelectModuleTest
37: [ RUN ] SelectModuleTest.BasicTest
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.BasicTest (18 ms)
37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (13 ms)
37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (12 ms)
37: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (13 ms)
37: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (14 ms)
37: [ RUN ] SelectModuleTest.NormalizesSizes
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.NormalizesSizes (11 ms)
37: [ RUN ] SelectModuleTest.WritesResidueNumbers
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.WritesResidueNumbers (8 ms)
37: [ RUN ] SelectModuleTest.WritesResidueIndices
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.WritesResidueIndices (8 ms)
37: [----------] 8 tests from SelectModuleTest (99 ms total)
37:
37: [----------] 10 tests from SurfaceAreaTest
37: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
37: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms)
37: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
37: [ OK ] SurfaceAreaTest.ComputesTwoPoints (3 ms)
37: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
37: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (2 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints12
37: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints32
37: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints42
37: [ OK ] SurfaceAreaTest.SurfacePoints42 (1 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints122
37: [ OK ] SurfaceAreaTest.SurfacePoints122 (2 ms)
37: [ RUN ] SurfaceAreaTest.Computes100Points
37: [ OK ] SurfaceAreaTest.Computes100Points (2 ms)
37: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
37: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (8 ms)
37: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
37: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (10 ms)
37: [----------] 10 tests from SurfaceAreaTest (29 ms total)
37:
37: [----------] 4 tests from TopologyInformation
37: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
37: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms)
37: [ RUN ] TopologyInformation.WorksWithGroFile
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TopologyInformation.WorksWithGroFile (8 ms)
37: [ RUN ] TopologyInformation.WorksWithPdbFile
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TopologyInformation.WorksWithPdbFile (9 ms)
37: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 1388140005
37: Generated 330891 of the 330891 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 330891 of the 330891 1-4 parameter combinations
37: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
37:
37: NOTE 2 [file lysozyme.top, line 1465]:
37: System has non-zero total charge: 2.000000
37: Total charge should normally be an integer. See
37: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
37: for discussion on how close it should be to an integer.
37:
37:
37:
37: Number of degrees of freedom in T-Coupling group rest is 465.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
37: Analysing residue names:
37: There are: 10 Protein residues
37: Analysing Protein...
37: This run will generate roughly 0 Mb of data
37: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (1179 ms)
37: [----------] 4 tests from TopologyInformation (1196 ms total)
37:
37: [----------] 4 tests from TrajectoryModuleTest
37: [ RUN ] TrajectoryModuleTest.BasicTest
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.BasicTest (11 ms)
37: [ RUN ] TrajectoryModuleTest.PlotsXOnly
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.PlotsXOnly (10 ms)
37: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (9 ms)
37: [ RUN ] TrajectoryModuleTest.HandlesNoForces
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.HandlesNoForces (9 ms)
37: [----------] 4 tests from TrajectoryModuleTest (39 ms total)
37:
37: [----------] 5 tests from UnionFinderTest
37: [ RUN ] UnionFinderTest.WorksEmpty
37: [ OK ] UnionFinderTest.WorksEmpty (0 ms)
37: [ RUN ] UnionFinderTest.BasicMerges
37: [ OK ] UnionFinderTest.BasicMerges (1 ms)
37: [ RUN ] UnionFinderTest.LargerMerges
37: [ OK ] UnionFinderTest.LargerMerges (0 ms)
37: [ RUN ] UnionFinderTest.LongRightMerge
37: [ OK ] UnionFinderTest.LongRightMerge (0 ms)
37: [ RUN ] UnionFinderTest.LongLeftMerge
37: [ OK ] UnionFinderTest.LongLeftMerge (0 ms)
37: [----------] 5 tests from UnionFinderTest (1 ms total)
37:
37: [----------] 1 test from MappedUnionFinderTest
37: [ RUN ] MappedUnionFinderTest.BasicMerges
37: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms)
37: [----------] 1 test from MappedUnionFinderTest (0 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 80 tests from 16 test cases ran. (3886 ms total)
37: [ PASSED ] 80 tests.
37/54 Test #37: TrajectoryAnalysisUnitTests ......... Passed 3.91 sec
test 38
Start 38: EnergyAnalysisUnitTests
38: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml"
38: Test timeout computed to be: 30
38: [==========] Running 7 tests from 4 test cases.
38: [----------] Global test environment set-up.
38: [----------] 1 test from DhdlTest
38: [ RUN ] DhdlTest.ExtractDhdl
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
38: Note: file tpx version 110, software tpx version 119
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
38:
38:
38: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
38: [ OK ] DhdlTest.ExtractDhdl (115 ms)
38: [----------] 1 test from DhdlTest (116 ms total)
38:
38: [----------] 1 test from OriresTest
38: [ RUN ] OriresTest.ExtractOrires
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
38: Note: file tpx version 111, software tpx version 119
38: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
38: End your selection with 0
38: Selecting all 7 orientation restraints
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
38: [ OK ] OriresTest.ExtractOrires (248 ms)
38: [----------] 1 test from OriresTest (248 ms total)
38:
38: [----------] 3 tests from EnergyTest
38: [ RUN ] EnergyTest.ExtractEnergy
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
38: Select the terms you want from the following list by
38: selecting either (part of) the name or the number or a combination.
38: End your selection with an empty line or a zero.
38: -------------------------------------------------------------------
38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
38: 13 Box-Z 14 Volume 15 Density 16 pV
38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
38:
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
38: [ OK ] EnergyTest.ExtractEnergy (26 ms)
38: [ RUN ] EnergyTest.ExtractEnergyByNumber
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
38: Select the terms you want from the following list by
38: selecting either (part of) the name or the number or a combination.
38: End your selection with an empty line or a zero.
38: -------------------------------------------------------------------
38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
38: 13 Box-Z 14 Volume 15 Density 16 pV
38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
38:
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
38: Pres. DC -268.49 3 8.52175 13.2804 (bar)
38: [ OK ] EnergyTest.ExtractEnergyByNumber (26 ms)
38: [ RUN ] EnergyTest.ExtractEnergyMixed
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
38: Select the terms you want from the following list by
38: selecting either (part of) the name or the number or a combination.
38: End your selection with an empty line or a zero.
38: -------------------------------------------------------------------
38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
38: 13 Box-Z 14 Volume 15 Density 16 pV
38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
38:
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
38: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
38: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
38: [ OK ] EnergyTest.ExtractEnergyMixed (26 ms)
38: [----------] 3 tests from EnergyTest (81 ms total)
38:
38: [----------] 2 tests from ViscosityTest
38: [ RUN ] ViscosityTest.EinsteinViscosity
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Pres-XX 20.2092 65 717.193 185.978 (bar)
38: Pres-XY -47.7351 39 372.522 207.456 (bar)
38: Pres-XZ 11.477 31 379.79 6.80818 (bar)
38: Pres-YX -47.7106 39 372.525 207.5 (bar)
38: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
38: Pres-YZ -41.3534 45 401.216 114.663 (bar)
38: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
38: Pres-ZY -41.3119 45 401.196 114.743 (bar)
38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
38: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
38: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
38: [ OK ] ViscosityTest.EinsteinViscosity (46 ms)
38: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Pres-XX 20.2092 65 717.193 185.978 (bar)
38: Pres-XY -47.7351 39 372.522 207.456 (bar)
38: Pres-XZ 11.477 31 379.79 6.80818 (bar)
38: Pres-YX -47.7106 39 372.525 207.5 (bar)
38: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
38: Pres-YZ -41.3534 45 401.216 114.663 (bar)
38: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
38: Pres-ZY -41.3119 45 401.196 114.743 (bar)
38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
38: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
38: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
38: [ OK ] ViscosityTest.EinsteinViscosityIntegral (42 ms)
38: [----------] 2 tests from ViscosityTest (89 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 7 tests from 4 test cases ran. (534 ms total)
38: [ PASSED ] 7 tests.
38/54 Test #38: EnergyAnalysisUnitTests ............. Passed 0.55 sec
test 39
Start 39: ToolUnitTests
39: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/ToolUnitTests.xml"
39: Test timeout computed to be: 30
39: [==========] Running 18 tests from 4 test cases.
39: [----------] Global test environment set-up.
39: [----------] 2 tests from DumpTest
39:
39: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
39: For a correct single-point energy evaluation with nsteps = 0, use
39: continuation = yes to avoid constraining the input coordinates.
39:
39: Setting the LD random seed to -1046041364
39: Generated 330891 of the 330891 non-bonded parameter combinations
39: Generating 1-4 interactions: fudge = 0.5
39: Generated 330891 of the 330891 1-4 parameter combinations
39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
39:
39: NOTE 2 [file lysozyme.top, line 1465]:
39: System has non-zero total charge: 2.000000
39: Total charge should normally be an integer. See
39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
39: for discussion on how close it should be to an integer.
39:
39:
39:
39: Number of degrees of freedom in T-Coupling group rest is 465.00
39:
39: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
39: NVE simulation with an initial temperature of zero: will use a Verlet
39: buffer of 10%. Check your energy drift!
39:
39:
39: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
39: You are using a plain Coulomb cut-off, which might produce artifacts.
39: You might want to consider using PME electrostatics.
39:
39:
39:
39: There were 4 notes
39: Analysing residue names:
39: There are: 10 Protein residues
39: Analysing Protein...
39: This run will generate roughly 0 Mb of data
39: [ RUN ] DumpTest.WorksWithTpr
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
39: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr:
39: inputrec:
39: integrator = md
39: tinit = 0
39: dt = 0.001
39: nsteps = 0
39: init-step = 0
39: simulation-part = 1
39: comm-mode = Linear
39: nstcomm = 100
39: bd-fric = 0
39: ld-seed = -1046041364
39: emtol = 10
39: emstep = 0.01
39: niter = 20
39: fcstep = 0
39: nstcgsteep = 1000
39: nbfgscorr = 10
39: rtpi = 0.05
39: nstxout = 0
39: nstvout = 0
39: nstfout = 0
39: nstlog = 1000
39: nstcalcenergy = 100
39: nstenergy = 1000
39: nstxout-compressed = 0
39: compressed-x-precision = 1000
39: cutoff-scheme = Verlet
39: nstlist = 10
39: pbc = xyz
39: periodic-molecules = false
39: verlet-buffer-tolerance = -1
39: rlist = 1.1
39: coulombtype = Cut-off
39: coulomb-modifier = Potential-shift
39: rcoulomb-switch = 0
39: rcoulomb = 1
39: epsilon-r = 1
39: epsilon-rf = inf
39: vdw-type = Cut-off
39: vdw-modifier = Potential-shift
39: rvdw-switch = 0
39: rvdw = 1
39: DispCorr = No
39: table-extension = 1
39: fourierspacing = 0.12
39: fourier-nx = 0
39: fourier-ny = 0
39: fourier-nz = 0
39: pme-order = 4
39: ewald-rtol = 1e-05
39: ewald-rtol-lj = 0.001
39: lj-pme-comb-rule = Geometric
39: ewald-geometry = 0
39: epsilon-surface = 0
39: tcoupl = No
39: nsttcouple = -1
39: nh-chain-length = 0
39: print-nose-hoover-chain-variables = false
39: pcoupl = No
39: pcoupltype = Isotropic
39: nstpcouple = -1
39: tau-p = 1
39: compressibility (3x3):
39: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: ref-p (3x3):
39: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: refcoord-scaling = No
39: posres-com (3):
39: posres-com[0]= 0.00000e+00
39: posres-com[1]= 0.00000e+00
39: posres-com[2]= 0.00000e+00
39: posres-comB (3):
39: posres-comB[0]= 0.00000e+00
39: posres-comB[1]= 0.00000e+00
39: posres-comB[2]= 0.00000e+00
39: QMMM = false
39: QMconstraints = 0
39: QMMMscheme = 0
39: MMChargeScaleFactor = 1
39: qm-opts:
39: ngQM = 0
39: constraint-algorithm = Lincs
39: continuation = false
39: Shake-SOR = false
39: shake-tol = 0.0001
39: lincs-order = 4
39: lincs-iter = 1
39: lincs-warnangle = 30
39: nwall = 0
39: wall-type = 9-3
39: wall-r-linpot = -1
39: wall-atomtype[0] = -1
39: wall-atomtype[1] = -1
39: wall-density[0] = 0
39: wall-density[1] = 0
39: wall-ewald-zfac = 3
39: pull = false
39: awh = false
39: rotation = false
39: interactiveMD = false
39: disre = No
39: disre-weighting = Conservative
39: disre-mixed = false
39: dr-fc = 1000
39: dr-tau = 0
39: nstdisreout = 100
39: orire-fc = 0
39: orire-tau = 0
39: nstorireout = 100
39: free-energy = no
39: cos-acceleration = 0
39: deform (3x3):
39: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: simulated-tempering = false
39: swapcoords = no
39: userint1 = 0
39: userint2 = 0
39: userint3 = 0
39: userint4 = 0
39: userreal1 = 0
39: userreal2 = 0
39: userreal3 = 0
39: userreal4 = 0
39: applied-forces:
39: electric-field:
39: x:
39: E0 = 0
39: omega = 0
39: t0 = 0
39: sigma = 0
39: y:
39: E0 = 0
39: omega = 0
39: t0 = 0
39: sigma = 0
39: z:
39: E0 = 0
39: omega = 0
39: t0 = 0
39: sigma = 0
39: density-guided-simulation:
39: active = false
39: group = protein
39: similarity-measure = inner-product
39: atom-spreading-weight = unity
39: force-constant = 1e+09
39: gaussian-transform-spreading-width = 0.2
39: gaussian-transform-spreading-range-in-multiples-of-width = 4
39: reference-density-filename = reference.mrc
39: nst = 1
39: normalize-densities = true
39: adaptive-force-scaling = false
39: adaptive-force-scaling-time-constant = 4
39: grpopts:
39: nrdf: 465
39: ref-t: 0
39: tau-t: 0
39: annealing: No
39: annealing-npoints: 0
39: acc: 0 0 0
39: nfreeze: N N N
39: energygrp-flags[ 0]: 0
39: header:
39: bIr = present
39: bBox = present
39: bTop = present
39: bX = present
39: bV = present
39: bF = not present
39: natoms = 156
39: lambda = 0.000000e+00
39: buffer size = 70122
39: topology:
39: name="First 10 residues from 1AKI"
39: #atoms = 156
39: #molblock = 1
39: molblock (0):
39: moltype = 0 "Protein_chain_B"
39: #molecules = 1
39: #posres_xA = 0
39: #posres_xB = 0
39: bIntermolecularInteractions = false
39: ffparams:
39: atnr=10
39: ntypes=212
39: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06
39: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06
39: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07
39: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06
39: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06
39: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06
39: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07
39: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07
39: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05
39: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06
39: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06
39: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07
39: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06
39: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06
39: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06
39: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07
39: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07
39: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05
39: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07
39: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07
39: functype[33]=LJ_SR, c6= 1.22578125e-04, c12= 2.99263000e-08
39: functype[34]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07
39: functype[35]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07
39: functype[36]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07
39: functype[37]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08
39: functype[38]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08
39: functype[39]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06
39: functype[40]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06
39: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[42]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06
39: functype[43]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07
39: functype[44]=LJ_SR, c6= 4.88684509e-03, c12= 1.35898974e-05
39: functype[45]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06
39: functype[46]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06
39: functype[47]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07
39: functype[48]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07
39: functype[49]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05
39: functype[50]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06
39: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[52]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06
39: functype[53]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07
39: functype[54]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06
39: functype[55]=LJ_SR, c6= 2.36385715e-03, c12= 1.58990617e-06
39: functype[56]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06
39: functype[57]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07
39: functype[58]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07
39: functype[59]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06
39: functype[60]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06
39: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[62]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06
39: functype[63]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07
39: functype[64]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06
39: functype[65]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06
39: functype[66]=LJ_SR, c6= 2.34487570e-03, c12= 4.69342567e-06
39: functype[67]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07
39: functype[68]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07
39: functype[69]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05
39: functype[70]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07
39: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[72]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07
39: functype[73]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08
39: functype[74]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07
39: functype[75]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07
39: functype[76]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07
39: functype[77]=LJ_SR, c6= 1.00847496e-04, c12= 2.02561691e-08
39: functype[78]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08
39: functype[79]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07
39: functype[80]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07
39: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[82]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07
39: functype[83]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08
39: functype[84]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07
39: functype[85]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07
39: functype[86]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07
39: functype[87]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08
39: functype[88]=LJ_SR, c6= 1.08571736e-04, c12= 1.40867851e-08
39: functype[89]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07
39: functype[90]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05
39: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[92]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05
39: functype[93]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06
39: functype[94]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05
39: functype[95]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06
39: functype[96]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05
39: functype[97]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07
39: functype[98]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07
39: functype[99]=LJ_SR, c6= 1.54830174e-02, c12= 3.37031588e-05
39: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05
39: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05
39: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05
39: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05
39: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05
39: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05
39: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05
39: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05
39: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05
39: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05
39: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05
39: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05
39: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05
39: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05
39: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05
39: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05
39: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02
39: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02
39: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02
39: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02
39: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02
39: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02
39: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02
39: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02
39: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02
39: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02
39: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02
39: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02
39: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02
39: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02
39: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02
39: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02
39: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02
39: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02
39: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02
39: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02
39: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02
39: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02
39: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02
39: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02
39: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2
39: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2
39: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2
39: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07
39: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06
39: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06
39: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06
39: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00
39: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07
39: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06
39: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08
39: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07
39: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06
39: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07
39: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06
39: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06
39: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06
39: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06
39: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07
39: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07
39: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07
39: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06
39: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06
39: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08
39: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07
39: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08
39: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06
39: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07
39: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05
39: reppow = 12
39: fudgeQQ = 0.5
39: cmap
39: atomtypes:
39: atomtype[ 0]={atomnumber= 7}
39: atomtype[ 1]={atomnumber= 1}
39: atomtype[ 2]={atomnumber= 6}
39: atomtype[ 3]={atomnumber= 1}
39: atomtype[ 4]={atomnumber= 6}
39: atomtype[ 5]={atomnumber= 8}
39: atomtype[ 6]={atomnumber= 6}
39: atomtype[ 7]={atomnumber= 1}
39: atomtype[ 8]={atomnumber= 6}
39: atomtype[ 9]={atomnumber= 16}
39: moltype (0):
39: name="Protein_chain_B"
39: atoms:
39: atom (156):
39: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
39: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6}
39: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
39: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
39: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
39: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6}
39: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
39: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6}
39: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8}
39: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7}
39: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1}
39: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6}
39: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6}
39: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
39: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
39: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6}
39: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8}
39: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7}
39: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1}
39: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6}
39: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
39: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6}
39: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
39: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
39: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6}
39: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8}
39: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7}
39: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1}
39: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6}
39: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
39: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
39: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6}
39: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8}
39: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1}
39: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6}
39: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6}
39: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6}
39: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6}
39: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1}
39: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6}
39: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6}
39: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8}
39: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7}
39: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1}
39: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6}
39: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
39: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6}
39: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
39: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
39: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16}
39: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1}
39: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6}
39: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8}
39: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7}
39: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1}
39: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6}
39: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6}
39: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6}
39: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6}
39: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
39: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
39: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6}
39: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8}
39: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7}
39: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1}
39: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6}
39: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6}
39: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6}
39: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
39: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
39: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6}
39: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8}
39: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7}
39: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1}
39: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6}
39: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6}
39: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6}
39: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8}
39: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7}
39: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1}
39: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6}
39: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6}
39: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6}
39: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8}
39: atom (156):
39: atom[0]={name="N"}
39: atom[1]={name="H1"}
39: atom[2]={name="H2"}
39: atom[3]={name="H3"}
39: atom[4]={name="CA"}
39: atom[5]={name="HA"}
39: atom[6]={name="CB"}
39: atom[7]={name="HB1"}
39: atom[8]={name="HB2"}
39: atom[9]={name="CG"}
39: atom[10]={name="HG1"}
39: atom[11]={name="HG2"}
39: atom[12]={name="CD"}
39: atom[13]={name="HD1"}
39: atom[14]={name="HD2"}
39: atom[15]={name="CE"}
39: atom[16]={name="HE1"}
39: atom[17]={name="HE2"}
39: atom[18]={name="NZ"}
39: atom[19]={name="HZ1"}
39: atom[20]={name="HZ2"}
39: atom[21]={name="HZ3"}
39: atom[22]={name="C"}
39: atom[23]={name="O"}
39: atom[24]={name="N"}
39: atom[25]={name="H"}
39: atom[26]={name="CA"}
39: atom[27]={name="HA"}
39: atom[28]={name="CB"}
39: atom[29]={name="HB"}
39: atom[30]={name="CG1"}
39: atom[31]={name="HG11"}
39: atom[32]={name="HG12"}
39: atom[33]={name="HG13"}
39: atom[34]={name="CG2"}
39: atom[35]={name="HG21"}
39: atom[36]={name="HG22"}
39: atom[37]={name="HG23"}
39: atom[38]={name="C"}
39: atom[39]={name="O"}
39: atom[40]={name="N"}
39: atom[41]={name="H"}
39: atom[42]={name="CA"}
39: atom[43]={name="HA"}
39: atom[44]={name="CB"}
39: atom[45]={name="HB1"}
39: atom[46]={name="HB2"}
39: atom[47]={name="CG"}
39: atom[48]={name="CD1"}
39: atom[49]={name="HD1"}
39: atom[50]={name="CD2"}
39: atom[51]={name="HD2"}
39: atom[52]={name="CE1"}
39: atom[53]={name="HE1"}
39: atom[54]={name="CE2"}
39: atom[55]={name="HE2"}
39: atom[56]={name="CZ"}
39: atom[57]={name="HZ"}
39: atom[58]={name="C"}
39: atom[59]={name="O"}
39: atom[60]={name="N"}
39: atom[61]={name="H"}
39: atom[62]={name="CA"}
39: atom[63]={name="HA1"}
39: atom[64]={name="HA2"}
39: atom[65]={name="C"}
39: atom[66]={name="O"}
39: atom[67]={name="N"}
39: atom[68]={name="H"}
39: atom[69]={name="CA"}
39: atom[70]={name="HA"}
39: atom[71]={name="CB"}
39: atom[72]={name="HB1"}
39: atom[73]={name="HB2"}
39: atom[74]={name="CG"}
39: atom[75]={name="HG1"}
39: atom[76]={name="HG2"}
39: atom[77]={name="CD"}
39: atom[78]={name="HD1"}
39: atom[79]={name="HD2"}
39: atom[80]={name="NE"}
39: atom[81]={name="HE"}
39: atom[82]={name="CZ"}
39: atom[83]={name="NH1"}
39: atom[84]={name="HH11"}
39: atom[85]={name="HH12"}
39: atom[86]={name="NH2"}
39: atom[87]={name="HH21"}
39: atom[88]={name="HH22"}
39: atom[89]={name="C"}
39: atom[90]={name="O"}
39: atom[91]={name="N"}
39: atom[92]={name="H"}
39: atom[93]={name="CA"}
39: atom[94]={name="HA"}
39: atom[95]={name="CB"}
39: atom[96]={name="HB1"}
39: atom[97]={name="HB2"}
39: atom[98]={name="SG"}
39: atom[99]={name="HG"}
39: atom[100]={name="C"}
39: atom[101]={name="O"}
39: atom[102]={name="N"}
39: atom[103]={name="H"}
39: atom[104]={name="CA"}
39: atom[105]={name="HA"}
39: atom[106]={name="CB"}
39: atom[107]={name="HB1"}
39: atom[108]={name="HB2"}
39: atom[109]={name="CG"}
39: atom[110]={name="HG1"}
39: atom[111]={name="HG2"}
39: atom[112]={name="CD"}
39: atom[113]={name="OE1"}
39: atom[114]={name="OE2"}
39: atom[115]={name="C"}
39: atom[116]={name="O"}
39: atom[117]={name="N"}
39: atom[118]={name="H"}
39: atom[119]={name="CA"}
39: atom[120]={name="HA"}
39: atom[121]={name="CB"}
39: atom[122]={name="HB1"}
39: atom[123]={name="HB2"}
39: atom[124]={name="CG"}
39: atom[125]={name="HG"}
39: atom[126]={name="CD1"}
39: atom[127]={name="HD11"}
39: atom[128]={name="HD12"}
39: atom[129]={name="HD13"}
39: atom[130]={name="CD2"}
39: atom[131]={name="HD21"}
39: atom[132]={name="HD22"}
39: atom[133]={name="HD23"}
39: atom[134]={name="C"}
39: atom[135]={name="O"}
39: atom[136]={name="N"}
39: atom[137]={name="H"}
39: atom[138]={name="CA"}
39: atom[139]={name="HA"}
39: atom[140]={name="CB"}
39: atom[141]={name="HB1"}
39: atom[142]={name="HB2"}
39: atom[143]={name="HB3"}
39: atom[144]={name="C"}
39: atom[145]={name="O"}
39: atom[146]={name="N"}
39: atom[147]={name="H"}
39: atom[148]={name="CA"}
39: atom[149]={name="HA"}
39: atom[150]={name="CB"}
39: atom[151]={name="HB1"}
39: atom[152]={name="HB2"}
39: atom[153]={name="HB3"}
39: atom[154]={name="C"}
39: atom[155]={name="O"}
39: type (156):
39: type[0]={name="opls_287",nameB="opls_287"}
39: type[1]={name="opls_290",nameB="opls_290"}
39: type[2]={name="opls_290",nameB="opls_290"}
39: type[3]={name="opls_290",nameB="opls_290"}
39: type[4]={name="opls_293B",nameB="opls_293B"}
39: type[5]={name="opls_140",nameB="opls_140"}
39: type[6]={name="opls_136",nameB="opls_136"}
39: type[7]={name="opls_140",nameB="opls_140"}
39: type[8]={name="opls_140",nameB="opls_140"}
39: type[9]={name="opls_136",nameB="opls_136"}
39: type[10]={name="opls_140",nameB="opls_140"}
39: type[11]={name="opls_140",nameB="opls_140"}
39: type[12]={name="opls_136",nameB="opls_136"}
39: type[13]={name="opls_140",nameB="opls_140"}
39: type[14]={name="opls_140",nameB="opls_140"}
39: type[15]={name="opls_292",nameB="opls_292"}
39: type[16]={name="opls_140",nameB="opls_140"}
39: type[17]={name="opls_140",nameB="opls_140"}
39: type[18]={name="opls_287",nameB="opls_287"}
39: type[19]={name="opls_290",nameB="opls_290"}
39: type[20]={name="opls_290",nameB="opls_290"}
39: type[21]={name="opls_290",nameB="opls_290"}
39: type[22]={name="opls_235",nameB="opls_235"}
39: type[23]={name="opls_236",nameB="opls_236"}
39: type[24]={name="opls_238",nameB="opls_238"}
39: type[25]={name="opls_241",nameB="opls_241"}
39: type[26]={name="opls_224B",nameB="opls_224B"}
39: type[27]={name="opls_140",nameB="opls_140"}
39: type[28]={name="opls_137",nameB="opls_137"}
39: type[29]={name="opls_140",nameB="opls_140"}
39: type[30]={name="opls_135",nameB="opls_135"}
39: type[31]={name="opls_140",nameB="opls_140"}
39: type[32]={name="opls_140",nameB="opls_140"}
39: type[33]={name="opls_140",nameB="opls_140"}
39: type[34]={name="opls_135",nameB="opls_135"}
39: type[35]={name="opls_140",nameB="opls_140"}
39: type[36]={name="opls_140",nameB="opls_140"}
39: type[37]={name="opls_140",nameB="opls_140"}
39: type[38]={name="opls_235",nameB="opls_235"}
39: type[39]={name="opls_236",nameB="opls_236"}
39: type[40]={name="opls_238",nameB="opls_238"}
39: type[41]={name="opls_241",nameB="opls_241"}
39: type[42]={name="opls_224B",nameB="opls_224B"}
39: type[43]={name="opls_140",nameB="opls_140"}
39: type[44]={name="opls_149",nameB="opls_149"}
39: type[45]={name="opls_140",nameB="opls_140"}
39: type[46]={name="opls_140",nameB="opls_140"}
39: type[47]={name="opls_145",nameB="opls_145"}
39: type[48]={name="opls_145",nameB="opls_145"}
39: type[49]={name="opls_146",nameB="opls_146"}
39: type[50]={name="opls_145",nameB="opls_145"}
39: type[51]={name="opls_146",nameB="opls_146"}
39: type[52]={name="opls_145",nameB="opls_145"}
39: type[53]={name="opls_146",nameB="opls_146"}
39: type[54]={name="opls_145",nameB="opls_145"}
39: type[55]={name="opls_146",nameB="opls_146"}
39: type[56]={name="opls_145",nameB="opls_145"}
39: type[57]={name="opls_146",nameB="opls_146"}
39: type[58]={name="opls_235",nameB="opls_235"}
39: type[59]={name="opls_236",nameB="opls_236"}
39: type[60]={name="opls_238",nameB="opls_238"}
39: type[61]={name="opls_241",nameB="opls_241"}
39: type[62]={name="opls_223B",nameB="opls_223B"}
39: type[63]={name="opls_140",nameB="opls_140"}
39: type[64]={name="opls_140",nameB="opls_140"}
39: type[65]={name="opls_235",nameB="opls_235"}
39: type[66]={name="opls_236",nameB="opls_236"}
39: type[67]={name="opls_238",nameB="opls_238"}
39: type[68]={name="opls_241",nameB="opls_241"}
39: type[69]={name="opls_224B",nameB="opls_224B"}
39: type[70]={name="opls_140",nameB="opls_140"}
39: type[71]={name="opls_136",nameB="opls_136"}
39: type[72]={name="opls_140",nameB="opls_140"}
39: type[73]={name="opls_140",nameB="opls_140"}
39: type[74]={name="opls_308",nameB="opls_308"}
39: type[75]={name="opls_140",nameB="opls_140"}
39: type[76]={name="opls_140",nameB="opls_140"}
39: type[77]={name="opls_307",nameB="opls_307"}
39: type[78]={name="opls_140",nameB="opls_140"}
39: type[79]={name="opls_140",nameB="opls_140"}
39: type[80]={name="opls_303",nameB="opls_303"}
39: type[81]={name="opls_304",nameB="opls_304"}
39: type[82]={name="opls_302",nameB="opls_302"}
39: type[83]={name="opls_300",nameB="opls_300"}
39: type[84]={name="opls_301",nameB="opls_301"}
39: type[85]={name="opls_301",nameB="opls_301"}
39: type[86]={name="opls_300",nameB="opls_300"}
39: type[87]={name="opls_301",nameB="opls_301"}
39: type[88]={name="opls_301",nameB="opls_301"}
39: type[89]={name="opls_235",nameB="opls_235"}
39: type[90]={name="opls_236",nameB="opls_236"}
39: type[91]={name="opls_238",nameB="opls_238"}
39: type[92]={name="opls_241",nameB="opls_241"}
39: type[93]={name="opls_224B",nameB="opls_224B"}
39: type[94]={name="opls_140",nameB="opls_140"}
39: type[95]={name="opls_206",nameB="opls_206"}
39: type[96]={name="opls_140",nameB="opls_140"}
39: type[97]={name="opls_140",nameB="opls_140"}
39: type[98]={name="opls_200",nameB="opls_200"}
39: type[99]={name="opls_204",nameB="opls_204"}
39: type[100]={name="opls_235",nameB="opls_235"}
39: type[101]={name="opls_236",nameB="opls_236"}
39: type[102]={name="opls_238",nameB="opls_238"}
39: type[103]={name="opls_241",nameB="opls_241"}
39: type[104]={name="opls_224B",nameB="opls_224B"}
39: type[105]={name="opls_140",nameB="opls_140"}
39: type[106]={name="opls_136",nameB="opls_136"}
39: type[107]={name="opls_140",nameB="opls_140"}
39: type[108]={name="opls_140",nameB="opls_140"}
39: type[109]={name="opls_274",nameB="opls_274"}
39: type[110]={name="opls_140",nameB="opls_140"}
39: type[111]={name="opls_140",nameB="opls_140"}
39: type[112]={name="opls_271",nameB="opls_271"}
39: type[113]={name="opls_272",nameB="opls_272"}
39: type[114]={name="opls_272",nameB="opls_272"}
39: type[115]={name="opls_235",nameB="opls_235"}
39: type[116]={name="opls_236",nameB="opls_236"}
39: type[117]={name="opls_238",nameB="opls_238"}
39: type[118]={name="opls_241",nameB="opls_241"}
39: type[119]={name="opls_224B",nameB="opls_224B"}
39: type[120]={name="opls_140",nameB="opls_140"}
39: type[121]={name="opls_136",nameB="opls_136"}
39: type[122]={name="opls_140",nameB="opls_140"}
39: type[123]={name="opls_140",nameB="opls_140"}
39: type[124]={name="opls_137",nameB="opls_137"}
39: type[125]={name="opls_140",nameB="opls_140"}
39: type[126]={name="opls_135",nameB="opls_135"}
39: type[127]={name="opls_140",nameB="opls_140"}
39: type[128]={name="opls_140",nameB="opls_140"}
39: type[129]={name="opls_140",nameB="opls_140"}
39: type[130]={name="opls_135",nameB="opls_135"}
39: type[131]={name="opls_140",nameB="opls_140"}
39: type[132]={name="opls_140",nameB="opls_140"}
39: type[133]={name="opls_140",nameB="opls_140"}
39: type[134]={name="opls_235",nameB="opls_235"}
39: type[135]={name="opls_236",nameB="opls_236"}
39: type[136]={name="opls_238",nameB="opls_238"}
39: type[137]={name="opls_241",nameB="opls_241"}
39: type[138]={name="opls_224B",nameB="opls_224B"}
39: type[139]={name="opls_140",nameB="opls_140"}
39: type[140]={name="opls_135",nameB="opls_135"}
39: type[141]={name="opls_140",nameB="opls_140"}
39: type[142]={name="opls_140",nameB="opls_140"}
39: type[143]={name="opls_140",nameB="opls_140"}
39: type[144]={name="opls_235",nameB="opls_235"}
39: type[145]={name="opls_236",nameB="opls_236"}
39: type[146]={name="opls_238",nameB="opls_238"}
39: type[147]={name="opls_241",nameB="opls_241"}
39: type[148]={name="opls_224B",nameB="opls_224B"}
39: type[149]={name="opls_140",nameB="opls_140"}
39: type[150]={name="opls_135",nameB="opls_135"}
39: type[151]={name="opls_140",nameB="opls_140"}
39: type[152]={name="opls_140",nameB="opls_140"}
39: type[153]={name="opls_140",nameB="opls_140"}
39: type[154]={name="opls_235",nameB="opls_235"}
39: type[155]={name="opls_236",nameB="opls_236"}
39: residue (10):
39: residue[0]={name="LYS", nr=1, ic=' '}
39: residue[1]={name="VAL", nr=2, ic=' '}
39: residue[2]={name="PHE", nr=3, ic=' '}
39: residue[3]={name="GLY", nr=4, ic=' '}
39: residue[4]={name="ARG", nr=5, ic=' '}
39: residue[5]={name="CYS", nr=6, ic=' '}
39: residue[6]={name="GLU", nr=7, ic=' '}
39: residue[7]={name="LEU", nr=8, ic=' '}
39: residue[8]={name="ALA", nr=9, ic=' '}
39: residue[9]={name="ALA", nr=10, ic=' '}
39: excls:
39: nr=156
39: nra=1828
39: excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
39: excls[1][13..20]={0, 1, 2, 3, 4, 5, 6, 22}
39: excls[2][21..28]={0, 1, 2, 3, 4, 5, 6, 22}
39: excls[3][29..36]={0, 1, 2, 3, 4, 5, 6, 22}
39: excls[4][37..54]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22,
39: 23, 24, 25, 26}
39: excls[5][55..67]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
39: excls[6][68..86]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
39: 14, 15, 22, 23, 24}
39: excls[7][87..97]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
39: excls[8][98..108]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
39: excls[9][109..125]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
39: 16, 17, 18, 22}
39: excls[10][126..136]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
39: excls[11][137..147]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
39: excls[12][148..164]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
39: 17, 18, 19, 20, 21}
39: excls[13][165..175]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
39: excls[14][176..186]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
39: excls[15][187..200]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
39: 19, 20, 21}
39: excls[16][201..211]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
39: excls[17][212..222]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
39: excls[18][223..233]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
39: excls[19][234..241]={12, 15, 16, 17, 18, 19, 20, 21}
39: excls[20][242..249]={12, 15, 16, 17, 18, 19, 20, 21}
39: excls[21][250..257]={12, 15, 16, 17, 18, 19, 20, 21}
39: excls[22][258..275]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24,
39: 25, 26, 27, 28, 38}
39: excls[23][276..284]={0, 4, 5, 6, 22, 23, 24, 25, 26}
39: excls[24][285..301]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29,
39: 30, 34, 38, 39, 40}
39: excls[25][302..310]={4, 22, 23, 24, 25, 26, 27, 28, 38}
39: excls[26][311..332]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
39: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42}
39: excls[27][333..344]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
39: 40}
39: excls[28][345..362]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
39: 34, 35, 36, 37, 38, 39, 40}
39: excls[29][363..376]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
39: 36, 37, 38}
39: excls[30][377..390]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
39: 36, 37, 38}
39: excls[31][391..398]={26, 28, 29, 30, 31, 32, 33, 34}
39: excls[32][399..406]={26, 28, 29, 30, 31, 32, 33, 34}
39: excls[33][407..414]={26, 28, 29, 30, 31, 32, 33, 34}
39: excls[34][415..428]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
39: 36, 37, 38}
39: excls[35][429..436]={26, 28, 29, 30, 34, 35, 36, 37}
39: excls[36][437..444]={26, 28, 29, 30, 34, 35, 36, 37}
39: excls[37][445..452]={26, 28, 29, 30, 34, 35, 36, 37}
39: excls[38][453..469]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
39: 40, 41, 42, 43, 44, 58}
39: excls[39][470..478]={24, 26, 27, 28, 38, 39, 40, 41, 42}
39: excls[40][479..495]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44,
39: 45, 46, 47, 58, 59, 60}
39: excls[41][496..504]={26, 38, 39, 40, 41, 42, 43, 44, 58}
39: excls[42][505..522]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
39: 48, 50, 58, 59, 60, 61, 62}
39: excls[43][523..534]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
39: 60}
39: excls[44][535..552]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
39: 50, 51, 52, 54, 58, 59, 60}
39: excls[45][553..562]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
39: excls[46][563..572]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
39: excls[47][573..589]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
39: 52, 53, 54, 55, 56, 58}
39: excls[48][590..603]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
39: 54, 56, 57}
39: excls[49][604..611]={44, 47, 48, 49, 50, 52, 53, 56}
39: excls[50][612..625]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54,
39: 55, 56, 57}
39: excls[51][626..633]={44, 47, 48, 50, 51, 54, 55, 56}
39: excls[52][634..644]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57}
39: excls[53][645..652]={47, 48, 49, 52, 53, 54, 56, 57}
39: excls[54][653..663]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57}
39: excls[55][664..671]={47, 50, 51, 52, 54, 55, 56, 57}
39: excls[56][672..682]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57}
39: excls[57][683..690]={48, 50, 52, 53, 54, 55, 56, 57}
39: excls[58][691..707]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
39: 60, 61, 62, 63, 64, 65}
39: excls[59][708..716]={40, 42, 43, 44, 58, 59, 60, 61, 62}
39: excls[60][717..730]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64,
39: 65, 66, 67}
39: excls[61][731..739]={42, 58, 59, 60, 61, 62, 63, 64, 65}
39: excls[62][740..752]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
39: 68, 69}
39: excls[63][753..761]={58, 60, 61, 62, 63, 64, 65, 66, 67}
39: excls[64][762..770]={58, 60, 61, 62, 63, 64, 65, 66, 67}
39: excls[65][771..784]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
39: 70, 71, 89}
39: excls[66][785..793]={60, 62, 63, 64, 65, 66, 67, 68, 69}
39: excls[67][794..810]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
39: 72, 73, 74, 89, 90, 91}
39: excls[68][811..819]={62, 65, 66, 67, 68, 69, 70, 71, 89}
39: excls[69][820..838]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
39: 75, 76, 77, 89, 90, 91, 92, 93}
39: excls[70][839..850]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
39: 91}
39: excls[71][851..868]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
39: 77, 78, 79, 80, 89, 90, 91}
39: excls[72][869..879]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
39: excls[73][880..890]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
39: excls[74][891..906]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
39: 79, 80, 81, 82, 89}
39: excls[75][907..917]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
39: excls[76][918..928]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
39: excls[77][929..943]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
39: 81, 82, 83, 86}
39: excls[78][944..953]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
39: excls[79][954..963]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
39: excls[80][964..979]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,
39: 84, 85, 86, 87, 88}
39: excls[81][980..988]={74, 77, 78, 79, 80, 81, 82, 83, 86}
39: excls[82][989..1001]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85,
39: 86, 87, 88}
39: excls[83][1002..1011]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
39: excls[84][1012..1017]={80, 82, 83, 84, 85, 86}
39: excls[85][1018..1023]={80, 82, 83, 84, 85, 86}
39: excls[86][1024..1033]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
39: excls[87][1034..1039]={80, 82, 83, 86, 87, 88}
39: excls[88][1040..1045]={80, 82, 83, 86, 87, 88}
39: excls[89][1046..1062]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89,
39: 90, 91, 92, 93, 94, 95, 100}
39: excls[90][1063..1071]={67, 69, 70, 71, 89, 90, 91, 92, 93}
39: excls[91][1072..1088]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94,
39: 95, 96, 97, 98, 100, 101, 102}
39: excls[92][1089..1097]={69, 89, 90, 91, 92, 93, 94, 95, 100}
39: excls[93][1098..1114]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97,
39: 98, 99, 100, 101, 102, 103, 104}
39: excls[94][1115..1126]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
39: 101, 102}
39: excls[95][1127..1139]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99,
39: 100, 101, 102}
39: excls[96][1140..1148]={91, 93, 94, 95, 96, 97, 98, 99, 100}
39: excls[97][1149..1157]={91, 93, 94, 95, 96, 97, 98, 99, 100}
39: excls[98][1158..1166]={91, 93, 94, 95, 96, 97, 98, 99, 100}
39: excls[99][1167..1172]={93, 95, 96, 97, 98, 99}
39: excls[100][1173..1189]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
39: 101, 102, 103, 104, 105, 106, 115}
39: excls[101][1190..1198]={91, 93, 94, 95, 100, 101, 102, 103, 104}
39: excls[102][1199..1215]={91, 93, 94, 95, 100, 101, 102, 103, 104,
39: 105, 106, 107, 108, 109, 115, 116, 117}
39: excls[103][1216..1224]={93, 100, 101, 102, 103, 104, 105, 106,
39: 115}
39: excls[104][1225..1243]={93, 100, 101, 102, 103, 104, 105, 106,
39: 107, 108, 109, 110, 111, 112, 115, 116, 117, 118, 119}
39: excls[105][1244..1255]={100, 102, 103, 104, 105, 106, 107, 108,
39: 109, 115, 116, 117}
39: excls[106][1256..1272]={100, 102, 103, 104, 105, 106, 107, 108,
39: 109, 110, 111, 112, 113, 114, 115, 116, 117}
39: excls[107][1273..1283]={102, 104, 105, 106, 107, 108, 109, 110,
39: 111, 112, 115}
39: excls[108][1284..1294]={102, 104, 105, 106, 107, 108, 109, 110,
39: 111, 112, 115}
39: excls[109][1295..1307]={102, 104, 105, 106, 107, 108, 109, 110,
39: 111, 112, 113, 114, 115}
39: excls[110][1308..1317]={104, 106, 107, 108, 109, 110, 111, 112,
39: 113, 114}
39: excls[111][1318..1327]={104, 106, 107, 108, 109, 110, 111, 112,
39: 113, 114}
39: excls[112][1328..1337]={104, 106, 107, 108, 109, 110, 111, 112,
39: 113, 114}
39: excls[113][1338..1344]={106, 109, 110, 111, 112, 113, 114}
39: excls[114][1345..1351]={106, 109, 110, 111, 112, 113, 114}
39: excls[115][1352..1368]={100, 102, 103, 104, 105, 106, 107, 108,
39: 109, 115, 116, 117, 118, 119, 120, 121, 134}
39: excls[116][1369..1377]={102, 104, 105, 106, 115, 116, 117, 118,
39: 119}
39: excls[117][1378..1394]={102, 104, 105, 106, 115, 116, 117, 118,
39: 119, 120, 121, 122, 123, 124, 134, 135, 136}
39: excls[118][1395..1403]={104, 115, 116, 117, 118, 119, 120, 121,
39: 134}
39: excls[119][1404..1422]={104, 115, 116, 117, 118, 119, 120, 121,
39: 122, 123, 124, 125, 126, 130, 134, 135, 136, 137, 138}
39: excls[120][1423..1434]={115, 117, 118, 119, 120, 121, 122, 123,
39: 124, 134, 135, 136}
39: excls[121][1435..1455]={115, 117, 118, 119, 120, 121, 122, 123,
39: 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135,
39: 136}
39: excls[122][1456..1466]={117, 119, 120, 121, 122, 123, 124, 125,
39: 126, 130, 134}
39: excls[123][1467..1477]={117, 119, 120, 121, 122, 123, 124, 125,
39: 126, 130, 134}
39: excls[124][1478..1494]={117, 119, 120, 121, 122, 123, 124, 125,
39: 126, 127, 128, 129, 130, 131, 132, 133, 134}
39: excls[125][1495..1508]={119, 121, 122, 123, 124, 125, 126, 127,
39: 128, 129, 130, 131, 132, 133}
39: excls[126][1509..1522]={119, 121, 122, 123, 124, 125, 126, 127,
39: 128, 129, 130, 131, 132, 133}
39: excls[127][1523..1530]={121, 124, 125, 126, 127, 128, 129, 130}
39: excls[128][1531..1538]={121, 124, 125, 126, 127, 128, 129, 130}
39: excls[129][1539..1546]={121, 124, 125, 126, 127, 128, 129, 130}
39: excls[130][1547..1560]={119, 121, 122, 123, 124, 125, 126, 127,
39: 128, 129, 130, 131, 132, 133}
39: excls[131][1561..1568]={121, 124, 125, 126, 130, 131, 132, 133}
39: excls[132][1569..1576]={121, 124, 125, 126, 130, 131, 132, 133}
39: excls[133][1577..1584]={121, 124, 125, 126, 130, 131, 132, 133}
39: excls[134][1585..1601]={115, 117, 118, 119, 120, 121, 122, 123,
39: 124, 134, 135, 136, 137, 138, 139, 140, 144}
39: excls[135][1602..1610]={117, 119, 120, 121, 134, 135, 136, 137,
39: 138}
39: excls[136][1611..1627]={117, 119, 120, 121, 134, 135, 136, 137,
39: 138, 139, 140, 141, 142, 143, 144, 145, 146}
39: excls[137][1628..1636]={119, 134, 135, 136, 137, 138, 139, 140,
39: 144}
39: excls[138][1637..1652]={119, 134, 135, 136, 137, 138, 139, 140,
39: 141, 142, 143, 144, 145, 146, 147, 148}
39: excls[139][1653..1664]={134, 136, 137, 138, 139, 140, 141, 142,
39: 143, 144, 145, 146}
39: excls[140][1665..1676]={134, 136, 137, 138, 139, 140, 141, 142,
39: 143, 144, 145, 146}
39: excls[141][1677..1684]={136, 138, 139, 140, 141, 142, 143, 144}
39: excls[142][1685..1692]={136, 138, 139, 140, 141, 142, 143, 144}
39: excls[143][1693..1700]={136, 138, 139, 140, 141, 142, 143, 144}
39: excls[144][1701..1717]={134, 136, 137, 138, 139, 140, 141, 142,
39: 143, 144, 145, 146, 147, 148, 149, 150, 154}
39: excls[145][1718..1726]={136, 138, 139, 140, 144, 145, 146, 147,
39: 148}
39: excls[146][1727..1742]={136, 138, 139, 140, 144, 145, 146, 147,
39: 148, 149, 150, 151, 152, 153, 154, 155}
39: excls[147][1743..1751]={138, 144, 145, 146, 147, 148, 149, 150,
39: 154}
39: excls[148][1752..1764]={138, 144, 145, 146, 147, 148, 149, 150,
39: 151, 152, 153, 154, 155}
39: excls[149][1765..1775]={144, 146, 147, 148, 149, 150, 151, 152,
39: 153, 154, 155}
39: excls[150][1776..1786]={144, 146, 147, 148, 149, 150, 151, 152,
39: 153, 154, 155}
39: excls[151][1787..1794]={146, 148, 149, 150, 151, 152, 153, 154}
39: excls[152][1795..1802]={146, 148, 149, 150, 151, 152, 153, 154}
39: excls[153][1803..1810]={146, 148, 149, 150, 151, 152, 153, 154}
39: excls[154][1811..1821]={144, 146, 147, 148, 149, 150, 151, 152,
39: 153, 154, 155}
39: excls[155][1822..1827]={146, 148, 149, 150, 154, 155}
39: Bond:
39: nr: 468
39: iatoms:
39: 0 type=100 (BONDS) 0 1
39: 1 type=100 (BONDS) 0 2
39: 2 type=100 (BONDS) 0 3
39: 3 type=101 (BONDS) 0 4
39: 4 type=102 (BONDS) 4 5
39: 5 type=103 (BONDS) 4 6
39: 6 type=104 (BONDS) 4 22
39: 7 type=102 (BONDS) 6 7
39: 8 type=102 (BONDS) 6 8
39: 9 type=103 (BONDS) 6 9
39: 10 type=102 (BONDS) 9 10
39: 11 type=102 (BONDS) 9 11
39: 12 type=103 (BONDS) 9 12
39: 13 type=102 (BONDS) 12 13
39: 14 type=102 (BONDS) 12 14
39: 15 type=103 (BONDS) 12 15
39: 16 type=102 (BONDS) 15 16
39: 17 type=102 (BONDS) 15 17
39: 18 type=101 (BONDS) 15 18
39: 19 type=100 (BONDS) 18 19
39: 20 type=100 (BONDS) 18 20
39: 21 type=100 (BONDS) 18 21
39: 22 type=105 (BONDS) 22 23
39: 23 type=106 (BONDS) 22 24
39: 24 type=100 (BONDS) 24 25
39: 25 type=107 (BONDS) 24 26
39: 26 type=102 (BONDS) 26 27
39: 27 type=103 (BONDS) 26 28
39: 28 type=104 (BONDS) 26 38
39: 29 type=102 (BONDS) 28 29
39: 30 type=103 (BONDS) 28 30
39: 31 type=103 (BONDS) 28 34
39: 32 type=102 (BONDS) 30 31
39: 33 type=102 (BONDS) 30 32
39: 34 type=102 (BONDS) 30 33
39: 35 type=102 (BONDS) 34 35
39: 36 type=102 (BONDS) 34 36
39: 37 type=102 (BONDS) 34 37
39: 38 type=105 (BONDS) 38 39
39: 39 type=106 (BONDS) 38 40
39: 40 type=100 (BONDS) 40 41
39: 41 type=107 (BONDS) 40 42
39: 42 type=102 (BONDS) 42 43
39: 43 type=103 (BONDS) 42 44
39: 44 type=104 (BONDS) 42 58
39: 45 type=102 (BONDS) 44 45
39: 46 type=102 (BONDS) 44 46
39: 47 type=108 (BONDS) 44 47
39: 48 type=109 (BONDS) 47 48
39: 49 type=109 (BONDS) 47 50
39: 50 type=110 (BONDS) 48 49
39: 51 type=109 (BONDS) 48 52
39: 52 type=110 (BONDS) 50 51
39: 53 type=109 (BONDS) 50 54
39: 54 type=110 (BONDS) 52 53
39: 55 type=109 (BONDS) 52 56
39: 56 type=110 (BONDS) 54 55
39: 57 type=109 (BONDS) 54 56
39: 58 type=110 (BONDS) 56 57
39: 59 type=105 (BONDS) 58 59
39: 60 type=106 (BONDS) 58 60
39: 61 type=100 (BONDS) 60 61
39: 62 type=107 (BONDS) 60 62
39: 63 type=102 (BONDS) 62 63
39: 64 type=102 (BONDS) 62 64
39: 65 type=104 (BONDS) 62 65
39: 66 type=105 (BONDS) 65 66
39: 67 type=106 (BONDS) 65 67
39: 68 type=100 (BONDS) 67 68
39: 69 type=107 (BONDS) 67 69
39: 70 type=102 (BONDS) 69 70
39: 71 type=103 (BONDS) 69 71
39: 72 type=104 (BONDS) 69 89
39: 73 type=102 (BONDS) 71 72
39: 74 type=102 (BONDS) 71 73
39: 75 type=103 (BONDS) 71 74
39: 76 type=102 (BONDS) 74 75
39: 77 type=102 (BONDS) 74 76
39: 78 type=103 (BONDS) 74 77
39: 79 type=102 (BONDS) 77 78
39: 80 type=102 (BONDS) 77 79
39: 81 type=111 (BONDS) 77 80
39: 82 type=100 (BONDS) 80 81
39: 83 type=112 (BONDS) 80 82
39: 84 type=112 (BONDS) 82 83
39: 85 type=112 (BONDS) 82 86
39: 86 type=100 (BONDS) 83 84
39: 87 type=100 (BONDS) 83 85
39: 88 type=100 (BONDS) 86 87
39: 89 type=100 (BONDS) 86 88
39: 90 type=105 (BONDS) 89 90
39: 91 type=106 (BONDS) 89 91
39: 92 type=100 (BONDS) 91 92
39: 93 type=107 (BONDS) 91 93
39: 94 type=102 (BONDS) 93 94
39: 95 type=103 (BONDS) 93 95
39: 96 type=104 (BONDS) 93 100
39: 97 type=102 (BONDS) 95 96
39: 98 type=102 (BONDS) 95 97
39: 99 type=113 (BONDS) 95 98
39: 100 type=114 (BONDS) 98 99
39: 101 type=105 (BONDS) 100 101
39: 102 type=106 (BONDS) 100 102
39: 103 type=100 (BONDS) 102 103
39: 104 type=107 (BONDS) 102 104
39: 105 type=102 (BONDS) 104 105
39: 106 type=103 (BONDS) 104 106
39: 107 type=104 (BONDS) 104 115
39: 108 type=102 (BONDS) 106 107
39: 109 type=102 (BONDS) 106 108
39: 110 type=103 (BONDS) 106 109
39: 111 type=102 (BONDS) 109 110
39: 112 type=102 (BONDS) 109 111
39: 113 type=104 (BONDS) 109 112
39: 114 type=115 (BONDS) 112 113
39: 115 type=115 (BONDS) 112 114
39: 116 type=105 (BONDS) 115 116
39: 117 type=106 (BONDS) 115 117
39: 118 type=100 (BONDS) 117 118
39: 119 type=107 (BONDS) 117 119
39: 120 type=102 (BONDS) 119 120
39: 121 type=103 (BONDS) 119 121
39: 122 type=104 (BONDS) 119 134
39: 123 type=102 (BONDS) 121 122
39: 124 type=102 (BONDS) 121 123
39: 125 type=103 (BONDS) 121 124
39: 126 type=102 (BONDS) 124 125
39: 127 type=103 (BONDS) 124 126
39: 128 type=103 (BONDS) 124 130
39: 129 type=102 (BONDS) 126 127
39: 130 type=102 (BONDS) 126 128
39: 131 type=102 (BONDS) 126 129
39: 132 type=102 (BONDS) 130 131
39: 133 type=102 (BONDS) 130 132
39: 134 type=102 (BONDS) 130 133
39: 135 type=105 (BONDS) 134 135
39: 136 type=106 (BONDS) 134 136
39: 137 type=100 (BONDS) 136 137
39: 138 type=107 (BONDS) 136 138
39: 139 type=102 (BONDS) 138 139
39: 140 type=103 (BONDS) 138 140
39: 141 type=104 (BONDS) 138 144
39: 142 type=102 (BONDS) 140 141
39: 143 type=102 (BONDS) 140 142
39: 144 type=102 (BONDS) 140 143
39: 145 type=105 (BONDS) 144 145
39: 146 type=106 (BONDS) 144 146
39: 147 type=100 (BONDS) 146 147
39: 148 type=107 (BONDS) 146 148
39: 149 type=102 (BONDS) 148 149
39: 150 type=103 (BONDS) 148 150
39: 151 type=104 (BONDS) 148 154
39: 152 type=102 (BONDS) 150 151
39: 153 type=102 (BONDS) 150 152
39: 154 type=102 (BONDS) 150 153
39: 155 type=105 (BONDS) 154 155
39: G96Bond:
39: nr: 0
39: Morse:
39: nr: 0
39: Cubic Bonds:
39: nr: 0
39: Connect Bonds:
39: nr: 0
39: Harmonic Pot.:
39: nr: 0
39: FENE Bonds:
39: nr: 0
39: Tab. Bonds:
39: nr: 0
39: Tab. Bonds NC:
39: nr: 0
39: Restraint Pot.:
39: nr: 0
39: Angle:
39: nr: 1124
39: iatoms:
39: 0 type=116 (ANGLES) 1 0 2
39: 1 type=116 (ANGLES) 1 0 3
39: 2 type=116 (ANGLES) 1 0 4
39: 3 type=116 (ANGLES) 2 0 3
39: 4 type=116 (ANGLES) 2 0 4
39: 5 type=116 (ANGLES) 3 0 4
39: 6 type=116 (ANGLES) 0 4 5
39: 7 type=117 (ANGLES) 0 4 6
39: 8 type=117 (ANGLES) 0 4 22
39: 9 type=118 (ANGLES) 5 4 6
39: 10 type=116 (ANGLES) 5 4 22
39: 11 type=119 (ANGLES) 6 4 22
39: 12 type=118 (ANGLES) 4 6 7
39: 13 type=118 (ANGLES) 4 6 8
39: 14 type=120 (ANGLES) 4 6 9
39: 15 type=121 (ANGLES) 7 6 8
39: 16 type=118 (ANGLES) 7 6 9
39: 17 type=118 (ANGLES) 8 6 9
39: 18 type=118 (ANGLES) 6 9 10
39: 19 type=118 (ANGLES) 6 9 11
39: 20 type=120 (ANGLES) 6 9 12
39: 21 type=121 (ANGLES) 10 9 11
39: 22 type=118 (ANGLES) 10 9 12
39: 23 type=118 (ANGLES) 11 9 12
39: 24 type=118 (ANGLES) 9 12 13
39: 25 type=118 (ANGLES) 9 12 14
39: 26 type=120 (ANGLES) 9 12 15
39: 27 type=121 (ANGLES) 13 12 14
39: 28 type=118 (ANGLES) 13 12 15
39: 29 type=118 (ANGLES) 14 12 15
39: 30 type=118 (ANGLES) 12 15 16
39: 31 type=118 (ANGLES) 12 15 17
39: 32 type=117 (ANGLES) 12 15 18
39: 33 type=121 (ANGLES) 16 15 17
39: 34 type=116 (ANGLES) 16 15 18
39: 35 type=116 (ANGLES) 17 15 18
39: 36 type=116 (ANGLES) 15 18 19
39: 37 type=116 (ANGLES) 15 18 20
39: 38 type=116 (ANGLES) 15 18 21
39: 39 type=116 (ANGLES) 19 18 20
39: 40 type=116 (ANGLES) 19 18 21
39: 41 type=116 (ANGLES) 20 18 21
39: 42 type=122 (ANGLES) 4 22 23
39: 43 type=123 (ANGLES) 4 22 24
39: 44 type=124 (ANGLES) 23 22 24
39: 45 type=125 (ANGLES) 22 24 25
39: 46 type=126 (ANGLES) 22 24 26
39: 47 type=127 (ANGLES) 25 24 26
39: 48 type=116 (ANGLES) 24 26 27
39: 49 type=128 (ANGLES) 24 26 28
39: 50 type=129 (ANGLES) 24 26 38
39: 51 type=118 (ANGLES) 27 26 28
39: 52 type=116 (ANGLES) 27 26 38
39: 53 type=119 (ANGLES) 28 26 38
39: 54 type=118 (ANGLES) 26 28 29
39: 55 type=120 (ANGLES) 26 28 30
39: 56 type=120 (ANGLES) 26 28 34
39: 57 type=118 (ANGLES) 29 28 30
39: 58 type=118 (ANGLES) 29 28 34
39: 59 type=120 (ANGLES) 30 28 34
39: 60 type=118 (ANGLES) 28 30 31
39: 61 type=118 (ANGLES) 28 30 32
39: 62 type=118 (ANGLES) 28 30 33
39: 63 type=121 (ANGLES) 31 30 32
39: 64 type=121 (ANGLES) 31 30 33
39: 65 type=121 (ANGLES) 32 30 33
39: 66 type=118 (ANGLES) 28 34 35
39: 67 type=118 (ANGLES) 28 34 36
39: 68 type=118 (ANGLES) 28 34 37
39: 69 type=121 (ANGLES) 35 34 36
39: 70 type=121 (ANGLES) 35 34 37
39: 71 type=121 (ANGLES) 36 34 37
39: 72 type=122 (ANGLES) 26 38 39
39: 73 type=123 (ANGLES) 26 38 40
39: 74 type=124 (ANGLES) 39 38 40
39: 75 type=125 (ANGLES) 38 40 41
39: 76 type=126 (ANGLES) 38 40 42
39: 77 type=127 (ANGLES) 41 40 42
39: 78 type=116 (ANGLES) 40 42 43
39: 79 type=128 (ANGLES) 40 42 44
39: 80 type=129 (ANGLES) 40 42 58
39: 81 type=118 (ANGLES) 43 42 44
39: 82 type=116 (ANGLES) 43 42 58
39: 83 type=119 (ANGLES) 44 42 58
39: 84 type=118 (ANGLES) 42 44 45
39: 85 type=118 (ANGLES) 42 44 46
39: 86 type=130 (ANGLES) 42 44 47
39: 87 type=121 (ANGLES) 45 44 46
39: 88 type=116 (ANGLES) 45 44 47
39: 89 type=116 (ANGLES) 46 44 47
39: 90 type=131 (ANGLES) 44 47 48
39: 91 type=131 (ANGLES) 44 47 50
39: 92 type=132 (ANGLES) 48 47 50
39: 93 type=133 (ANGLES) 47 48 49
39: 94 type=132 (ANGLES) 47 48 52
39: 95 type=133 (ANGLES) 49 48 52
39: 96 type=133 (ANGLES) 47 50 51
39: 97 type=132 (ANGLES) 47 50 54
39: 98 type=133 (ANGLES) 51 50 54
39: 99 type=133 (ANGLES) 48 52 53
39: 100 type=132 (ANGLES) 48 52 56
39: 101 type=133 (ANGLES) 53 52 56
39: 102 type=133 (ANGLES) 50 54 55
39: 103 type=132 (ANGLES) 50 54 56
39: 104 type=133 (ANGLES) 55 54 56
39: 105 type=132 (ANGLES) 52 56 54
39: 106 type=133 (ANGLES) 52 56 57
39: 107 type=133 (ANGLES) 54 56 57
39: 108 type=122 (ANGLES) 42 58 59
39: 109 type=123 (ANGLES) 42 58 60
39: 110 type=124 (ANGLES) 59 58 60
39: 111 type=125 (ANGLES) 58 60 61
39: 112 type=126 (ANGLES) 58 60 62
39: 113 type=127 (ANGLES) 61 60 62
39: 114 type=116 (ANGLES) 60 62 63
39: 115 type=116 (ANGLES) 60 62 64
39: 116 type=129 (ANGLES) 60 62 65
39: 117 type=121 (ANGLES) 63 62 64
39: 118 type=116 (ANGLES) 63 62 65
39: 119 type=116 (ANGLES) 64 62 65
39: 120 type=122 (ANGLES) 62 65 66
39: 121 type=123 (ANGLES) 62 65 67
39: 122 type=124 (ANGLES) 66 65 67
39: 123 type=125 (ANGLES) 65 67 68
39: 124 type=126 (ANGLES) 65 67 69
39: 125 type=127 (ANGLES) 68 67 69
39: 126 type=116 (ANGLES) 67 69 70
39: 127 type=128 (ANGLES) 67 69 71
39: 128 type=129 (ANGLES) 67 69 89
39: 129 type=118 (ANGLES) 70 69 71
39: 130 type=116 (ANGLES) 70 69 89
39: 131 type=119 (ANGLES) 71 69 89
39: 132 type=118 (ANGLES) 69 71 72
39: 133 type=118 (ANGLES) 69 71 73
39: 134 type=120 (ANGLES) 69 71 74
39: 135 type=121 (ANGLES) 72 71 73
39: 136 type=118 (ANGLES) 72 71 74
39: 137 type=118 (ANGLES) 73 71 74
39: 138 type=118 (ANGLES) 71 74 75
39: 139 type=118 (ANGLES) 71 74 76
39: 140 type=120 (ANGLES) 71 74 77
39: 141 type=121 (ANGLES) 75 74 76
39: 142 type=118 (ANGLES) 75 74 77
39: 143 type=118 (ANGLES) 76 74 77
39: 144 type=118 (ANGLES) 74 77 78
39: 145 type=118 (ANGLES) 74 77 79
39: 146 type=117 (ANGLES) 74 77 80
39: 147 type=121 (ANGLES) 78 77 79
39: 148 type=116 (ANGLES) 78 77 80
39: 149 type=116 (ANGLES) 79 77 80
39: 150 type=134 (ANGLES) 77 80 81
39: 151 type=135 (ANGLES) 77 80 82
39: 152 type=133 (ANGLES) 81 80 82
39: 153 type=131 (ANGLES) 80 82 83
39: 154 type=131 (ANGLES) 80 82 86
39: 155 type=131 (ANGLES) 83 82 86
39: 156 type=133 (ANGLES) 82 83 84
39: 157 type=133 (ANGLES) 82 83 85
39: 158 type=133 (ANGLES) 84 83 85
39: 159 type=133 (ANGLES) 82 86 87
39: 160 type=133 (ANGLES) 82 86 88
39: 161 type=133 (ANGLES) 87 86 88
39: 162 type=122 (ANGLES) 69 89 90
39: 163 type=123 (ANGLES) 69 89 91
39: 164 type=124 (ANGLES) 90 89 91
39: 165 type=125 (ANGLES) 89 91 92
39: 166 type=126 (ANGLES) 89 91 93
39: 167 type=127 (ANGLES) 92 91 93
39: 168 type=116 (ANGLES) 91 93 94
39: 169 type=128 (ANGLES) 91 93 95
39: 170 type=129 (ANGLES) 91 93 100
39: 171 type=118 (ANGLES) 94 93 95
39: 172 type=116 (ANGLES) 94 93 100
39: 173 type=119 (ANGLES) 95 93 100
39: 174 type=118 (ANGLES) 93 95 96
39: 175 type=118 (ANGLES) 93 95 97
39: 176 type=136 (ANGLES) 93 95 98
39: 177 type=121 (ANGLES) 96 95 97
39: 178 type=116 (ANGLES) 96 95 98
39: 179 type=116 (ANGLES) 97 95 98
39: 180 type=137 (ANGLES) 95 98 99
39: 181 type=122 (ANGLES) 93 100 101
39: 182 type=123 (ANGLES) 93 100 102
39: 183 type=124 (ANGLES) 101 100 102
39: 184 type=125 (ANGLES) 100 102 103
39: 185 type=126 (ANGLES) 100 102 104
39: 186 type=127 (ANGLES) 103 102 104
39: 187 type=116 (ANGLES) 102 104 105
39: 188 type=128 (ANGLES) 102 104 106
39: 189 type=129 (ANGLES) 102 104 115
39: 190 type=118 (ANGLES) 105 104 106
39: 191 type=116 (ANGLES) 105 104 115
39: 192 type=119 (ANGLES) 106 104 115
39: 193 type=118 (ANGLES) 104 106 107
39: 194 type=118 (ANGLES) 104 106 108
39: 195 type=120 (ANGLES) 104 106 109
39: 196 type=121 (ANGLES) 107 106 108
39: 197 type=118 (ANGLES) 107 106 109
39: 198 type=118 (ANGLES) 108 106 109
39: 199 type=118 (ANGLES) 106 109 110
39: 200 type=118 (ANGLES) 106 109 111
39: 201 type=119 (ANGLES) 106 109 112
39: 202 type=121 (ANGLES) 110 109 111
39: 203 type=116 (ANGLES) 110 109 112
39: 204 type=116 (ANGLES) 111 109 112
39: 205 type=138 (ANGLES) 109 112 113
39: 206 type=138 (ANGLES) 109 112 114
39: 207 type=139 (ANGLES) 113 112 114
39: 208 type=122 (ANGLES) 104 115 116
39: 209 type=123 (ANGLES) 104 115 117
39: 210 type=124 (ANGLES) 116 115 117
39: 211 type=125 (ANGLES) 115 117 118
39: 212 type=126 (ANGLES) 115 117 119
39: 213 type=127 (ANGLES) 118 117 119
39: 214 type=116 (ANGLES) 117 119 120
39: 215 type=128 (ANGLES) 117 119 121
39: 216 type=129 (ANGLES) 117 119 134
39: 217 type=118 (ANGLES) 120 119 121
39: 218 type=116 (ANGLES) 120 119 134
39: 219 type=119 (ANGLES) 121 119 134
39: 220 type=118 (ANGLES) 119 121 122
39: 221 type=118 (ANGLES) 119 121 123
39: 222 type=120 (ANGLES) 119 121 124
39: 223 type=121 (ANGLES) 122 121 123
39: 224 type=118 (ANGLES) 122 121 124
39: 225 type=118 (ANGLES) 123 121 124
39: 226 type=118 (ANGLES) 121 124 125
39: 227 type=120 (ANGLES) 121 124 126
39: 228 type=120 (ANGLES) 121 124 130
39: 229 type=118 (ANGLES) 125 124 126
39: 230 type=118 (ANGLES) 125 124 130
39: 231 type=120 (ANGLES) 126 124 130
39: 232 type=118 (ANGLES) 124 126 127
39: 233 type=118 (ANGLES) 124 126 128
39: 234 type=118 (ANGLES) 124 126 129
39: 235 type=121 (ANGLES) 127 126 128
39: 236 type=121 (ANGLES) 127 126 129
39: 237 type=121 (ANGLES) 128 126 129
39: 238 type=118 (ANGLES) 124 130 131
39: 239 type=118 (ANGLES) 124 130 132
39: 240 type=118 (ANGLES) 124 130 133
39: 241 type=121 (ANGLES) 131 130 132
39: 242 type=121 (ANGLES) 131 130 133
39: 243 type=121 (ANGLES) 132 130 133
39: 244 type=122 (ANGLES) 119 134 135
39: 245 type=123 (ANGLES) 119 134 136
39: 246 type=124 (ANGLES) 135 134 136
39: 247 type=125 (ANGLES) 134 136 137
39: 248 type=126 (ANGLES) 134 136 138
39: 249 type=127 (ANGLES) 137 136 138
39: 250 type=116 (ANGLES) 136 138 139
39: 251 type=128 (ANGLES) 136 138 140
39: 252 type=129 (ANGLES) 136 138 144
39: 253 type=118 (ANGLES) 139 138 140
39: 254 type=116 (ANGLES) 139 138 144
39: 255 type=119 (ANGLES) 140 138 144
39: 256 type=118 (ANGLES) 138 140 141
39: 257 type=118 (ANGLES) 138 140 142
39: 258 type=118 (ANGLES) 138 140 143
39: 259 type=121 (ANGLES) 141 140 142
39: 260 type=121 (ANGLES) 141 140 143
39: 261 type=121 (ANGLES) 142 140 143
39: 262 type=122 (ANGLES) 138 144 145
39: 263 type=123 (ANGLES) 138 144 146
39: 264 type=124 (ANGLES) 145 144 146
39: 265 type=125 (ANGLES) 144 146 147
39: 266 type=126 (ANGLES) 144 146 148
39: 267 type=127 (ANGLES) 147 146 148
39: 268 type=116 (ANGLES) 146 148 149
39: 269 type=128 (ANGLES) 146 148 150
39: 270 type=129 (ANGLES) 146 148 154
39: 271 type=118 (ANGLES) 149 148 150
39: 272 type=116 (ANGLES) 149 148 154
39: 273 type=119 (ANGLES) 150 148 154
39: 274 type=118 (ANGLES) 148 150 151
39: 275 type=118 (ANGLES) 148 150 152
39: 276 type=118 (ANGLES) 148 150 153
39: 277 type=121 (ANGLES) 151 150 152
39: 278 type=121 (ANGLES) 151 150 153
39: 279 type=121 (ANGLES) 152 150 153
39: 280 type=122 (ANGLES) 148 154 155
39: G96Angle:
39: nr: 0
39: Restricted Angles:
39: nr: 0
39: Lin. Angle:
39: nr: 0
39: Bond-Cross:
39: nr: 0
39: BA-Cross:
39: nr: 0
39: U-B:
39: nr: 0
39: Quartic Angles:
39: nr: 0
39: Tab. Angles:
39: nr: 0
39: Proper Dih.:
39: nr: 145
39: iatoms:
39: 0 type=140 (PDIHS) 4 24 22 23
39: 1 type=141 (PDIHS) 22 26 24 25
39: 2 type=140 (PDIHS) 26 40 38 39
39: 3 type=141 (PDIHS) 38 42 40 41
39: 4 type=140 (PDIHS) 42 60 58 59
39: 5 type=142 (PDIHS) 44 47 50 48
39: 6 type=142 (PDIHS) 47 52 48 49
39: 7 type=142 (PDIHS) 47 54 50 51
39: 8 type=142 (PDIHS) 48 56 52 53
39: 9 type=142 (PDIHS) 50 56 54 55
39: 10 type=142 (PDIHS) 52 54 56 57
39: 11 type=141 (PDIHS) 58 62 60 61
39: 12 type=140 (PDIHS) 62 67 65 66
39: 13 type=141 (PDIHS) 65 69 67 68
39: 14 type=140 (PDIHS) 69 91 89 90
39: 15 type=141 (PDIHS) 77 82 80 81
39: 16 type=140 (PDIHS) 80 83 82 86
39: 17 type=141 (PDIHS) 82 84 83 85
39: 18 type=141 (PDIHS) 82 87 86 88
39: 19 type=141 (PDIHS) 89 93 91 92
39: 20 type=140 (PDIHS) 93 102 100 101
39: 21 type=141 (PDIHS) 100 104 102 103
39: 22 type=140 (PDIHS) 104 117 115 116
39: 23 type=140 (PDIHS) 109 113 112 114
39: 24 type=141 (PDIHS) 115 119 117 118
39: 25 type=140 (PDIHS) 119 136 134 135
39: 26 type=141 (PDIHS) 134 138 136 137
39: 27 type=140 (PDIHS) 138 146 144 145
39: 28 type=141 (PDIHS) 144 148 146 147
39: Ryckaert-Bell.:
39: nr: 1565
39: iatoms:
39: 0 type=143 (RBDIHS) 1 0 4 5
39: 1 type=144 (RBDIHS) 1 0 4 6
39: 2 type=144 (RBDIHS) 1 0 4 22
39: 3 type=143 (RBDIHS) 2 0 4 5
39: 4 type=144 (RBDIHS) 2 0 4 6
39: 5 type=144 (RBDIHS) 2 0 4 22
39: 6 type=143 (RBDIHS) 3 0 4 5
39: 7 type=144 (RBDIHS) 3 0 4 6
39: 8 type=144 (RBDIHS) 3 0 4 22
39: 9 type=145 (RBDIHS) 0 4 6 9
39: 10 type=146 (RBDIHS) 22 4 6 9
39: 11 type=147 (RBDIHS) 0 4 6 7
39: 12 type=147 (RBDIHS) 0 4 6 8
39: 13 type=148 (RBDIHS) 5 4 6 7
39: 14 type=148 (RBDIHS) 5 4 6 8
39: 15 type=148 (RBDIHS) 5 4 6 9
39: 16 type=149 (RBDIHS) 22 4 6 7
39: 17 type=149 (RBDIHS) 22 4 6 8
39: 18 type=150 (RBDIHS) 0 4 22 24
39: 19 type=151 (RBDIHS) 6 4 22 24
39: 20 type=148 (RBDIHS) 4 6 9 10
39: 21 type=148 (RBDIHS) 4 6 9 11
39: 22 type=152 (RBDIHS) 4 6 9 12
39: 23 type=148 (RBDIHS) 7 6 9 10
39: 24 type=148 (RBDIHS) 7 6 9 11
39: 25 type=148 (RBDIHS) 7 6 9 12
39: 26 type=148 (RBDIHS) 8 6 9 10
39: 27 type=148 (RBDIHS) 8 6 9 11
39: 28 type=148 (RBDIHS) 8 6 9 12
39: 29 type=148 (RBDIHS) 6 9 12 13
39: 30 type=148 (RBDIHS) 6 9 12 14
39: 31 type=152 (RBDIHS) 6 9 12 15
39: 32 type=148 (RBDIHS) 10 9 12 13
39: 33 type=148 (RBDIHS) 10 9 12 14
39: 34 type=148 (RBDIHS) 10 9 12 15
39: 35 type=148 (RBDIHS) 11 9 12 13
39: 36 type=148 (RBDIHS) 11 9 12 14
39: 37 type=148 (RBDIHS) 11 9 12 15
39: 38 type=148 (RBDIHS) 9 12 15 16
39: 39 type=148 (RBDIHS) 9 12 15 17
39: 40 type=153 (RBDIHS) 9 12 15 18
39: 41 type=148 (RBDIHS) 13 12 15 16
39: 42 type=148 (RBDIHS) 13 12 15 17
39: 43 type=154 (RBDIHS) 13 12 15 18
39: 44 type=148 (RBDIHS) 14 12 15 16
39: 45 type=148 (RBDIHS) 14 12 15 17
39: 46 type=154 (RBDIHS) 14 12 15 18
39: 47 type=144 (RBDIHS) 12 15 18 19
39: 48 type=144 (RBDIHS) 12 15 18 20
39: 49 type=144 (RBDIHS) 12 15 18 21
39: 50 type=143 (RBDIHS) 16 15 18 19
39: 51 type=143 (RBDIHS) 16 15 18 20
39: 52 type=143 (RBDIHS) 16 15 18 21
39: 53 type=143 (RBDIHS) 17 15 18 19
39: 54 type=143 (RBDIHS) 17 15 18 20
39: 55 type=143 (RBDIHS) 17 15 18 21
39: 56 type=155 (RBDIHS) 4 22 24 25
39: 57 type=156 (RBDIHS) 4 22 24 26
39: 58 type=155 (RBDIHS) 23 22 24 25
39: 59 type=157 (RBDIHS) 23 22 24 26
39: 60 type=158 (RBDIHS) 22 24 26 28
39: 61 type=159 (RBDIHS) 22 24 26 38
39: 62 type=160 (RBDIHS) 24 26 28 30
39: 63 type=160 (RBDIHS) 24 26 28 34
39: 64 type=161 (RBDIHS) 38 26 28 30
39: 65 type=161 (RBDIHS) 38 26 28 34
39: 66 type=147 (RBDIHS) 24 26 28 29
39: 67 type=148 (RBDIHS) 27 26 28 29
39: 68 type=148 (RBDIHS) 27 26 28 30
39: 69 type=148 (RBDIHS) 27 26 28 34
39: 70 type=149 (RBDIHS) 38 26 28 29
39: 71 type=150 (RBDIHS) 24 26 38 40
39: 72 type=151 (RBDIHS) 28 26 38 40
39: 73 type=148 (RBDIHS) 26 28 30 31
39: 74 type=148 (RBDIHS) 26 28 30 32
39: 75 type=148 (RBDIHS) 26 28 30 33
39: 76 type=148 (RBDIHS) 29 28 30 31
39: 77 type=148 (RBDIHS) 29 28 30 32
39: 78 type=148 (RBDIHS) 29 28 30 33
39: 79 type=148 (RBDIHS) 34 28 30 31
39: 80 type=148 (RBDIHS) 34 28 30 32
39: 81 type=148 (RBDIHS) 34 28 30 33
39: 82 type=148 (RBDIHS) 26 28 34 35
39: 83 type=148 (RBDIHS) 26 28 34 36
39: 84 type=148 (RBDIHS) 26 28 34 37
39: 85 type=148 (RBDIHS) 29 28 34 35
39: 86 type=148 (RBDIHS) 29 28 34 36
39: 87 type=148 (RBDIHS) 29 28 34 37
39: 88 type=148 (RBDIHS) 30 28 34 35
39: 89 type=148 (RBDIHS) 30 28 34 36
39: 90 type=148 (RBDIHS) 30 28 34 37
39: 91 type=155 (RBDIHS) 26 38 40 41
39: 92 type=156 (RBDIHS) 26 38 40 42
39: 93 type=155 (RBDIHS) 39 38 40 41
39: 94 type=157 (RBDIHS) 39 38 40 42
39: 95 type=158 (RBDIHS) 38 40 42 44
39: 96 type=159 (RBDIHS) 38 40 42 58
39: 97 type=147 (RBDIHS) 40 42 44 45
39: 98 type=147 (RBDIHS) 40 42 44 46
39: 99 type=162 (RBDIHS) 40 42 44 47
39: 100 type=148 (RBDIHS) 43 42 44 45
39: 101 type=148 (RBDIHS) 43 42 44 46
39: 102 type=163 (RBDIHS) 43 42 44 47
39: 103 type=149 (RBDIHS) 58 42 44 45
39: 104 type=149 (RBDIHS) 58 42 44 46
39: 105 type=164 (RBDIHS) 58 42 44 47
39: 106 type=150 (RBDIHS) 40 42 58 60
39: 107 type=151 (RBDIHS) 44 42 58 60
39: 108 type=165 (RBDIHS) 44 47 48 49
39: 109 type=165 (RBDIHS) 44 47 48 52
39: 110 type=165 (RBDIHS) 50 47 48 49
39: 111 type=165 (RBDIHS) 50 47 48 52
39: 112 type=165 (RBDIHS) 44 47 50 51
39: 113 type=165 (RBDIHS) 44 47 50 54
39: 114 type=165 (RBDIHS) 48 47 50 51
39: 115 type=165 (RBDIHS) 48 47 50 54
39: 116 type=165 (RBDIHS) 47 48 52 53
39: 117 type=165 (RBDIHS) 47 48 52 56
39: 118 type=165 (RBDIHS) 49 48 52 53
39: 119 type=165 (RBDIHS) 49 48 52 56
39: 120 type=165 (RBDIHS) 47 50 54 55
39: 121 type=165 (RBDIHS) 47 50 54 56
39: 122 type=165 (RBDIHS) 51 50 54 55
39: 123 type=165 (RBDIHS) 51 50 54 56
39: 124 type=165 (RBDIHS) 48 52 56 54
39: 125 type=165 (RBDIHS) 48 52 56 57
39: 126 type=165 (RBDIHS) 53 52 56 54
39: 127 type=165 (RBDIHS) 53 52 56 57
39: 128 type=165 (RBDIHS) 50 54 56 52
39: 129 type=165 (RBDIHS) 50 54 56 57
39: 130 type=165 (RBDIHS) 55 54 56 52
39: 131 type=165 (RBDIHS) 55 54 56 57
39: 132 type=155 (RBDIHS) 42 58 60 61
39: 133 type=156 (RBDIHS) 42 58 60 62
39: 134 type=155 (RBDIHS) 59 58 60 61
39: 135 type=157 (RBDIHS) 59 58 60 62
39: 136 type=159 (RBDIHS) 58 60 62 65
39: 137 type=150 (RBDIHS) 60 62 65 67
39: 138 type=155 (RBDIHS) 62 65 67 68
39: 139 type=156 (RBDIHS) 62 65 67 69
39: 140 type=155 (RBDIHS) 66 65 67 68
39: 141 type=157 (RBDIHS) 66 65 67 69
39: 142 type=158 (RBDIHS) 65 67 69 71
39: 143 type=159 (RBDIHS) 65 67 69 89
39: 144 type=166 (RBDIHS) 67 69 71 74
39: 145 type=167 (RBDIHS) 89 69 71 74
39: 146 type=147 (RBDIHS) 67 69 71 72
39: 147 type=147 (RBDIHS) 67 69 71 73
39: 148 type=148 (RBDIHS) 70 69 71 72
39: 149 type=148 (RBDIHS) 70 69 71 73
39: 150 type=148 (RBDIHS) 70 69 71 74
39: 151 type=149 (RBDIHS) 89 69 71 72
39: 152 type=149 (RBDIHS) 89 69 71 73
39: 153 type=150 (RBDIHS) 67 69 89 91
39: 154 type=151 (RBDIHS) 71 69 89 91
39: 155 type=148 (RBDIHS) 69 71 74 75
39: 156 type=148 (RBDIHS) 69 71 74 76
39: 157 type=152 (RBDIHS) 69 71 74 77
39: 158 type=148 (RBDIHS) 72 71 74 75
39: 159 type=148 (RBDIHS) 72 71 74 76
39: 160 type=148 (RBDIHS) 72 71 74 77
39: 161 type=148 (RBDIHS) 73 71 74 75
39: 162 type=148 (RBDIHS) 73 71 74 76
39: 163 type=148 (RBDIHS) 73 71 74 77
39: 164 type=148 (RBDIHS) 71 74 77 78
39: 165 type=148 (RBDIHS) 71 74 77 79
39: 166 type=153 (RBDIHS) 71 74 77 80
39: 167 type=148 (RBDIHS) 75 74 77 78
39: 168 type=148 (RBDIHS) 75 74 77 79
39: 169 type=168 (RBDIHS) 75 74 77 80
39: 170 type=148 (RBDIHS) 76 74 77 78
39: 171 type=148 (RBDIHS) 76 74 77 79
39: 172 type=168 (RBDIHS) 76 74 77 80
39: 173 type=169 (RBDIHS) 74 77 80 81
39: 174 type=170 (RBDIHS) 74 77 80 82
39: 175 type=171 (RBDIHS) 78 77 80 82
39: 176 type=171 (RBDIHS) 79 77 80 82
39: 177 type=172 (RBDIHS) 77 80 82 83
39: 178 type=172 (RBDIHS) 77 80 82 86
39: 179 type=173 (RBDIHS) 81 80 82 83
39: 180 type=173 (RBDIHS) 81 80 82 86
39: 181 type=173 (RBDIHS) 80 82 83 84
39: 182 type=173 (RBDIHS) 80 82 83 85
39: 183 type=173 (RBDIHS) 86 82 83 84
39: 184 type=173 (RBDIHS) 86 82 83 85
39: 185 type=173 (RBDIHS) 80 82 86 87
39: 186 type=173 (RBDIHS) 80 82 86 88
39: 187 type=173 (RBDIHS) 83 82 86 87
39: 188 type=173 (RBDIHS) 83 82 86 88
39: 189 type=155 (RBDIHS) 69 89 91 92
39: 190 type=156 (RBDIHS) 69 89 91 93
39: 191 type=155 (RBDIHS) 90 89 91 92
39: 192 type=157 (RBDIHS) 90 89 91 93
39: 193 type=158 (RBDIHS) 89 91 93 95
39: 194 type=159 (RBDIHS) 89 91 93 100
39: 195 type=174 (RBDIHS) 91 93 95 98
39: 196 type=175 (RBDIHS) 100 93 95 98
39: 197 type=147 (RBDIHS) 91 93 95 96
39: 198 type=147 (RBDIHS) 91 93 95 97
39: 199 type=148 (RBDIHS) 94 93 95 96
39: 200 type=148 (RBDIHS) 94 93 95 97
39: 201 type=176 (RBDIHS) 94 93 95 98
39: 202 type=149 (RBDIHS) 100 93 95 96
39: 203 type=149 (RBDIHS) 100 93 95 97
39: 204 type=150 (RBDIHS) 91 93 100 102
39: 205 type=151 (RBDIHS) 95 93 100 102
39: 206 type=177 (RBDIHS) 93 95 98 99
39: 207 type=178 (RBDIHS) 96 95 98 99
39: 208 type=178 (RBDIHS) 97 95 98 99
39: 209 type=155 (RBDIHS) 93 100 102 103
39: 210 type=156 (RBDIHS) 93 100 102 104
39: 211 type=155 (RBDIHS) 101 100 102 103
39: 212 type=157 (RBDIHS) 101 100 102 104
39: 213 type=158 (RBDIHS) 100 102 104 106
39: 214 type=159 (RBDIHS) 100 102 104 115
39: 215 type=179 (RBDIHS) 102 104 106 109
39: 216 type=180 (RBDIHS) 115 104 106 109
39: 217 type=147 (RBDIHS) 102 104 106 107
39: 218 type=147 (RBDIHS) 102 104 106 108
39: 219 type=148 (RBDIHS) 105 104 106 107
39: 220 type=148 (RBDIHS) 105 104 106 108
39: 221 type=148 (RBDIHS) 105 104 106 109
39: 222 type=149 (RBDIHS) 115 104 106 107
39: 223 type=149 (RBDIHS) 115 104 106 108
39: 224 type=150 (RBDIHS) 102 104 115 117
39: 225 type=151 (RBDIHS) 106 104 115 117
39: 226 type=148 (RBDIHS) 104 106 109 110
39: 227 type=148 (RBDIHS) 104 106 109 111
39: 228 type=181 (RBDIHS) 104 106 109 112
39: 229 type=148 (RBDIHS) 107 106 109 110
39: 230 type=148 (RBDIHS) 107 106 109 111
39: 231 type=182 (RBDIHS) 107 106 109 112
39: 232 type=148 (RBDIHS) 108 106 109 110
39: 233 type=148 (RBDIHS) 108 106 109 111
39: 234 type=182 (RBDIHS) 108 106 109 112
39: 235 type=183 (RBDIHS) 106 109 112 113
39: 236 type=183 (RBDIHS) 106 109 112 114
39: 237 type=155 (RBDIHS) 104 115 117 118
39: 238 type=156 (RBDIHS) 104 115 117 119
39: 239 type=155 (RBDIHS) 116 115 117 118
39: 240 type=157 (RBDIHS) 116 115 117 119
39: 241 type=158 (RBDIHS) 115 117 119 121
39: 242 type=159 (RBDIHS) 115 117 119 134
39: 243 type=184 (RBDIHS) 117 119 121 124
39: 244 type=185 (RBDIHS) 134 119 121 124
39: 245 type=147 (RBDIHS) 117 119 121 122
39: 246 type=147 (RBDIHS) 117 119 121 123
39: 247 type=148 (RBDIHS) 120 119 121 122
39: 248 type=148 (RBDIHS) 120 119 121 123
39: 249 type=148 (RBDIHS) 120 119 121 124
39: 250 type=149 (RBDIHS) 134 119 121 122
39: 251 type=149 (RBDIHS) 134 119 121 123
39: 252 type=150 (RBDIHS) 117 119 134 136
39: 253 type=151 (RBDIHS) 121 119 134 136
39: 254 type=148 (RBDIHS) 119 121 124 125
39: 255 type=152 (RBDIHS) 119 121 124 126
39: 256 type=152 (RBDIHS) 119 121 124 130
39: 257 type=148 (RBDIHS) 122 121 124 125
39: 258 type=148 (RBDIHS) 122 121 124 126
39: 259 type=148 (RBDIHS) 122 121 124 130
39: 260 type=148 (RBDIHS) 123 121 124 125
39: 261 type=148 (RBDIHS) 123 121 124 126
39: 262 type=148 (RBDIHS) 123 121 124 130
39: 263 type=148 (RBDIHS) 121 124 126 127
39: 264 type=148 (RBDIHS) 121 124 126 128
39: 265 type=148 (RBDIHS) 121 124 126 129
39: 266 type=148 (RBDIHS) 125 124 126 127
39: 267 type=148 (RBDIHS) 125 124 126 128
39: 268 type=148 (RBDIHS) 125 124 126 129
39: 269 type=148 (RBDIHS) 130 124 126 127
39: 270 type=148 (RBDIHS) 130 124 126 128
39: 271 type=148 (RBDIHS) 130 124 126 129
39: 272 type=148 (RBDIHS) 121 124 130 131
39: 273 type=148 (RBDIHS) 121 124 130 132
39: 274 type=148 (RBDIHS) 121 124 130 133
39: 275 type=148 (RBDIHS) 125 124 130 131
39: 276 type=148 (RBDIHS) 125 124 130 132
39: 277 type=148 (RBDIHS) 125 124 130 133
39: 278 type=148 (RBDIHS) 126 124 130 131
39: 279 type=148 (RBDIHS) 126 124 130 132
39: 280 type=148 (RBDIHS) 126 124 130 133
39: 281 type=155 (RBDIHS) 119 134 136 137
39: 282 type=156 (RBDIHS) 119 134 136 138
39: 283 type=155 (RBDIHS) 135 134 136 137
39: 284 type=157 (RBDIHS) 135 134 136 138
39: 285 type=158 (RBDIHS) 134 136 138 140
39: 286 type=159 (RBDIHS) 134 136 138 144
39: 287 type=147 (RBDIHS) 136 138 140 141
39: 288 type=147 (RBDIHS) 136 138 140 142
39: 289 type=147 (RBDIHS) 136 138 140 143
39: 290 type=148 (RBDIHS) 139 138 140 141
39: 291 type=148 (RBDIHS) 139 138 140 142
39: 292 type=148 (RBDIHS) 139 138 140 143
39: 293 type=149 (RBDIHS) 144 138 140 141
39: 294 type=149 (RBDIHS) 144 138 140 142
39: 295 type=149 (RBDIHS) 144 138 140 143
39: 296 type=150 (RBDIHS) 136 138 144 146
39: 297 type=151 (RBDIHS) 140 138 144 146
39: 298 type=155 (RBDIHS) 138 144 146 147
39: 299 type=156 (RBDIHS) 138 144 146 148
39: 300 type=155 (RBDIHS) 145 144 146 147
39: 301 type=157 (RBDIHS) 145 144 146 148
39: 302 type=158 (RBDIHS) 144 146 148 150
39: 303 type=159 (RBDIHS) 144 146 148 154
39: 304 type=147 (RBDIHS) 146 148 150 151
39: 305 type=147 (RBDIHS) 146 148 150 152
39: 306 type=147 (RBDIHS) 146 148 150 153
39: 307 type=148 (RBDIHS) 149 148 150 151
39: 308 type=148 (RBDIHS) 149 148 150 152
39: 309 type=148 (RBDIHS) 149 148 150 153
39: 310 type=149 (RBDIHS) 154 148 150 151
39: 311 type=149 (RBDIHS) 154 148 150 152
39: 312 type=149 (RBDIHS) 154 148 150 153
39: Restricted Dih.:
39: nr: 0
39: CBT Dih.:
39: nr: 0
39: Fourier Dih.:
39: nr: 0
39: Improper Dih.:
39: nr: 0
39: Improper Dih.:
39: nr: 0
39: Tab. Dih.:
39: nr: 0
39: CMAP Dih.:
39: nr: 0
39: GB 1-2 Pol. (unused):
39: nr: 0
39: GB 1-3 Pol. (unused):
39: nr: 0
39: GB 1-4 Pol. (unused):
39: nr: 0
39: GB Polarization (unused):
39: nr: 0
39: Nonpolar Sol. (unused):
39: nr: 0
39: LJ-14:
39: nr: 1197
39: iatoms:
39: 0 type=186 (LJ14) 0 7
39: 1 type=186 (LJ14) 0 8
39: 2 type=187 (LJ14) 0 9
39: 3 type=188 (LJ14) 0 23
39: 4 type=189 (LJ14) 0 24
39: 5 type=190 (LJ14) 1 5
39: 6 type=190 (LJ14) 1 6
39: 7 type=190 (LJ14) 1 22
39: 8 type=190 (LJ14) 2 5
39: 9 type=190 (LJ14) 2 6
39: 10 type=190 (LJ14) 2 22
39: 11 type=190 (LJ14) 3 5
39: 12 type=190 (LJ14) 3 6
39: 13 type=190 (LJ14) 3 22
39: 14 type=191 (LJ14) 4 10
39: 15 type=191 (LJ14) 4 11
39: 16 type=192 (LJ14) 4 12
39: 17 type=190 (LJ14) 4 25
39: 18 type=192 (LJ14) 4 26
39: 19 type=193 (LJ14) 5 7
39: 20 type=193 (LJ14) 5 8
39: 21 type=191 (LJ14) 5 9
39: 22 type=194 (LJ14) 5 23
39: 23 type=186 (LJ14) 5 24
39: 24 type=191 (LJ14) 6 13
39: 25 type=191 (LJ14) 6 14
39: 26 type=192 (LJ14) 6 15
39: 27 type=195 (LJ14) 6 23
39: 28 type=187 (LJ14) 6 24
39: 29 type=193 (LJ14) 7 10
39: 30 type=193 (LJ14) 7 11
39: 31 type=191 (LJ14) 7 12
39: 32 type=196 (LJ14) 7 22
39: 33 type=193 (LJ14) 8 10
39: 34 type=193 (LJ14) 8 11
39: 35 type=191 (LJ14) 8 12
39: 36 type=196 (LJ14) 8 22
39: 37 type=191 (LJ14) 9 16
39: 38 type=191 (LJ14) 9 17
39: 39 type=187 (LJ14) 9 18
39: 40 type=197 (LJ14) 9 22
39: 41 type=193 (LJ14) 10 13
39: 42 type=193 (LJ14) 10 14
39: 43 type=191 (LJ14) 10 15
39: 44 type=193 (LJ14) 11 13
39: 45 type=193 (LJ14) 11 14
39: 46 type=191 (LJ14) 11 15
39: 47 type=190 (LJ14) 12 19
39: 48 type=190 (LJ14) 12 20
39: 49 type=190 (LJ14) 12 21
39: 50 type=193 (LJ14) 13 16
39: 51 type=193 (LJ14) 13 17
39: 52 type=186 (LJ14) 13 18
39: 53 type=193 (LJ14) 14 16
39: 54 type=193 (LJ14) 14 17
39: 55 type=186 (LJ14) 14 18
39: 56 type=190 (LJ14) 16 19
39: 57 type=190 (LJ14) 16 20
39: 58 type=190 (LJ14) 16 21
39: 59 type=190 (LJ14) 17 19
39: 60 type=190 (LJ14) 17 20
39: 61 type=190 (LJ14) 17 21
39: 62 type=196 (LJ14) 22 27
39: 63 type=197 (LJ14) 22 28
39: 64 type=198 (LJ14) 22 38
39: 65 type=190 (LJ14) 23 25
39: 66 type=195 (LJ14) 23 26
39: 67 type=186 (LJ14) 24 29
39: 68 type=187 (LJ14) 24 30
39: 69 type=187 (LJ14) 24 34
39: 70 type=188 (LJ14) 24 39
39: 71 type=189 (LJ14) 24 40
39: 72 type=190 (LJ14) 25 27
39: 73 type=190 (LJ14) 25 28
39: 74 type=190 (LJ14) 25 38
39: 75 type=191 (LJ14) 26 31
39: 76 type=191 (LJ14) 26 32
39: 77 type=191 (LJ14) 26 33
39: 78 type=191 (LJ14) 26 35
39: 79 type=191 (LJ14) 26 36
39: 80 type=191 (LJ14) 26 37
39: 81 type=190 (LJ14) 26 41
39: 82 type=192 (LJ14) 26 42
39: 83 type=193 (LJ14) 27 29
39: 84 type=191 (LJ14) 27 30
39: 85 type=191 (LJ14) 27 34
39: 86 type=194 (LJ14) 27 39
39: 87 type=186 (LJ14) 27 40
39: 88 type=195 (LJ14) 28 39
39: 89 type=187 (LJ14) 28 40
39: 90 type=193 (LJ14) 29 31
39: 91 type=193 (LJ14) 29 32
39: 92 type=193 (LJ14) 29 33
39: 93 type=193 (LJ14) 29 35
39: 94 type=193 (LJ14) 29 36
39: 95 type=193 (LJ14) 29 37
39: 96 type=196 (LJ14) 29 38
39: 97 type=191 (LJ14) 30 35
39: 98 type=191 (LJ14) 30 36
39: 99 type=191 (LJ14) 30 37
39: 100 type=197 (LJ14) 30 38
39: 101 type=191 (LJ14) 31 34
39: 102 type=191 (LJ14) 32 34
39: 103 type=191 (LJ14) 33 34
39: 104 type=197 (LJ14) 34 38
39: 105 type=196 (LJ14) 38 43
39: 106 type=197 (LJ14) 38 44
39: 107 type=198 (LJ14) 38 58
39: 108 type=190 (LJ14) 39 41
39: 109 type=195 (LJ14) 39 42
39: 110 type=186 (LJ14) 40 45
39: 111 type=186 (LJ14) 40 46
39: 112 type=199 (LJ14) 40 47
39: 113 type=188 (LJ14) 40 59
39: 114 type=189 (LJ14) 40 60
39: 115 type=190 (LJ14) 41 43
39: 116 type=190 (LJ14) 41 44
39: 117 type=190 (LJ14) 41 58
39: 118 type=200 (LJ14) 42 48
39: 119 type=200 (LJ14) 42 50
39: 120 type=190 (LJ14) 42 61
39: 121 type=192 (LJ14) 42 62
39: 122 type=193 (LJ14) 43 45
39: 123 type=193 (LJ14) 43 46
39: 124 type=201 (LJ14) 43 47
39: 125 type=194 (LJ14) 43 59
39: 126 type=186 (LJ14) 43 60
39: 127 type=202 (LJ14) 44 49
39: 128 type=202 (LJ14) 44 51
39: 129 type=200 (LJ14) 44 52
39: 130 type=200 (LJ14) 44 54
39: 131 type=195 (LJ14) 44 59
39: 132 type=187 (LJ14) 44 60
39: 133 type=201 (LJ14) 45 48
39: 134 type=201 (LJ14) 45 50
39: 135 type=196 (LJ14) 45 58
39: 136 type=201 (LJ14) 46 48
39: 137 type=201 (LJ14) 46 50
39: 138 type=196 (LJ14) 46 58
39: 139 type=203 (LJ14) 47 53
39: 140 type=203 (LJ14) 47 55
39: 141 type=204 (LJ14) 47 56
39: 142 type=205 (LJ14) 47 58
39: 143 type=203 (LJ14) 48 51
39: 144 type=204 (LJ14) 48 54
39: 145 type=203 (LJ14) 48 57
39: 146 type=203 (LJ14) 49 50
39: 147 type=206 (LJ14) 49 53
39: 148 type=203 (LJ14) 49 56
39: 149 type=204 (LJ14) 50 52
39: 150 type=203 (LJ14) 50 57
39: 151 type=206 (LJ14) 51 55
39: 152 type=203 (LJ14) 51 56
39: 153 type=203 (LJ14) 52 55
39: 154 type=203 (LJ14) 53 54
39: 155 type=206 (LJ14) 53 57
39: 156 type=206 (LJ14) 55 57
39: 157 type=196 (LJ14) 58 63
39: 158 type=196 (LJ14) 58 64
39: 159 type=198 (LJ14) 58 65
39: 160 type=190 (LJ14) 59 61
39: 161 type=195 (LJ14) 59 62
39: 162 type=188 (LJ14) 60 66
39: 163 type=189 (LJ14) 60 67
39: 164 type=190 (LJ14) 61 63
39: 165 type=190 (LJ14) 61 64
39: 166 type=190 (LJ14) 61 65
39: 167 type=190 (LJ14) 62 68
39: 168 type=192 (LJ14) 62 69
39: 169 type=194 (LJ14) 63 66
39: 170 type=186 (LJ14) 63 67
39: 171 type=194 (LJ14) 64 66
39: 172 type=186 (LJ14) 64 67
39: 173 type=196 (LJ14) 65 70
39: 174 type=197 (LJ14) 65 71
39: 175 type=198 (LJ14) 65 89
39: 176 type=190 (LJ14) 66 68
39: 177 type=195 (LJ14) 66 69
39: 178 type=186 (LJ14) 67 72
39: 179 type=186 (LJ14) 67 73
39: 180 type=187 (LJ14) 67 74
39: 181 type=188 (LJ14) 67 90
39: 182 type=189 (LJ14) 67 91
39: 183 type=190 (LJ14) 68 70
39: 184 type=190 (LJ14) 68 71
39: 185 type=190 (LJ14) 68 89
39: 186 type=191 (LJ14) 69 75
39: 187 type=191 (LJ14) 69 76
39: 188 type=192 (LJ14) 69 77
39: 189 type=190 (LJ14) 69 92
39: 190 type=192 (LJ14) 69 93
39: 191 type=193 (LJ14) 70 72
39: 192 type=193 (LJ14) 70 73
39: 193 type=191 (LJ14) 70 74
39: 194 type=194 (LJ14) 70 90
39: 195 type=186 (LJ14) 70 91
39: 196 type=191 (LJ14) 71 78
39: 197 type=191 (LJ14) 71 79
39: 198 type=187 (LJ14) 71 80
39: 199 type=195 (LJ14) 71 90
39: 200 type=187 (LJ14) 71 91
39: 201 type=193 (LJ14) 72 75
39: 202 type=193 (LJ14) 72 76
39: 203 type=191 (LJ14) 72 77
39: 204 type=196 (LJ14) 72 89
39: 205 type=193 (LJ14) 73 75
39: 206 type=193 (LJ14) 73 76
39: 207 type=191 (LJ14) 73 77
39: 208 type=196 (LJ14) 73 89
39: 209 type=190 (LJ14) 74 81
39: 210 type=207 (LJ14) 74 82
39: 211 type=197 (LJ14) 74 89
39: 212 type=193 (LJ14) 75 78
39: 213 type=193 (LJ14) 75 79
39: 214 type=186 (LJ14) 75 80
39: 215 type=193 (LJ14) 76 78
39: 216 type=193 (LJ14) 76 79
39: 217 type=186 (LJ14) 76 80
39: 218 type=187 (LJ14) 77 83
39: 219 type=187 (LJ14) 77 86
39: 220 type=190 (LJ14) 78 81
39: 221 type=208 (LJ14) 78 82
39: 222 type=190 (LJ14) 79 81
39: 223 type=208 (LJ14) 79 82
39: 224 type=190 (LJ14) 80 84
39: 225 type=190 (LJ14) 80 85
39: 226 type=190 (LJ14) 80 87
39: 227 type=190 (LJ14) 80 88
39: 228 type=190 (LJ14) 81 83
39: 229 type=190 (LJ14) 81 86
39: 230 type=190 (LJ14) 83 87
39: 231 type=190 (LJ14) 83 88
39: 232 type=190 (LJ14) 84 86
39: 233 type=190 (LJ14) 85 86
39: 234 type=196 (LJ14) 89 94
39: 235 type=197 (LJ14) 89 95
39: 236 type=198 (LJ14) 89 100
39: 237 type=190 (LJ14) 90 92
39: 238 type=195 (LJ14) 90 93
39: 239 type=186 (LJ14) 91 96
39: 240 type=186 (LJ14) 91 97
39: 241 type=209 (LJ14) 91 98
39: 242 type=188 (LJ14) 91 101
39: 243 type=189 (LJ14) 91 102
39: 244 type=190 (LJ14) 92 94
39: 245 type=190 (LJ14) 92 95
39: 246 type=190 (LJ14) 92 100
39: 247 type=190 (LJ14) 93 99
39: 248 type=190 (LJ14) 93 103
39: 249 type=192 (LJ14) 93 104
39: 250 type=193 (LJ14) 94 96
39: 251 type=193 (LJ14) 94 97
39: 252 type=210 (LJ14) 94 98
39: 253 type=194 (LJ14) 94 101
39: 254 type=186 (LJ14) 94 102
39: 255 type=195 (LJ14) 95 101
39: 256 type=187 (LJ14) 95 102
39: 257 type=190 (LJ14) 96 99
39: 258 type=196 (LJ14) 96 100
39: 259 type=190 (LJ14) 97 99
39: 260 type=196 (LJ14) 97 100
39: 261 type=211 (LJ14) 98 100
39: 262 type=196 (LJ14) 100 105
39: 263 type=197 (LJ14) 100 106
39: 264 type=198 (LJ14) 100 115
39: 265 type=190 (LJ14) 101 103
39: 266 type=195 (LJ14) 101 104
39: 267 type=186 (LJ14) 102 107
39: 268 type=186 (LJ14) 102 108
39: 269 type=187 (LJ14) 102 109
39: 270 type=188 (LJ14) 102 116
39: 271 type=189 (LJ14) 102 117
39: 272 type=190 (LJ14) 103 105
39: 273 type=190 (LJ14) 103 106
39: 274 type=190 (LJ14) 103 115
39: 275 type=191 (LJ14) 104 110
39: 276 type=191 (LJ14) 104 111
39: 277 type=197 (LJ14) 104 112
39: 278 type=190 (LJ14) 104 118
39: 279 type=192 (LJ14) 104 119
39: 280 type=193 (LJ14) 105 107
39: 281 type=193 (LJ14) 105 108
39: 282 type=191 (LJ14) 105 109
39: 283 type=194 (LJ14) 105 116
39: 284 type=186 (LJ14) 105 117
39: 285 type=195 (LJ14) 106 113
39: 286 type=195 (LJ14) 106 114
39: 287 type=195 (LJ14) 106 116
39: 288 type=187 (LJ14) 106 117
39: 289 type=193 (LJ14) 107 110
39: 290 type=193 (LJ14) 107 111
39: 291 type=196 (LJ14) 107 112
39: 292 type=196 (LJ14) 107 115
39: 293 type=193 (LJ14) 108 110
39: 294 type=193 (LJ14) 108 111
39: 295 type=196 (LJ14) 108 112
39: 296 type=196 (LJ14) 108 115
39: 297 type=197 (LJ14) 109 115
39: 298 type=194 (LJ14) 110 113
39: 299 type=194 (LJ14) 110 114
39: 300 type=194 (LJ14) 111 113
39: 301 type=194 (LJ14) 111 114
39: 302 type=196 (LJ14) 115 120
39: 303 type=197 (LJ14) 115 121
39: 304 type=198 (LJ14) 115 134
39: 305 type=190 (LJ14) 116 118
39: 306 type=195 (LJ14) 116 119
39: 307 type=186 (LJ14) 117 122
39: 308 type=186 (LJ14) 117 123
39: 309 type=187 (LJ14) 117 124
39: 310 type=188 (LJ14) 117 135
39: 311 type=189 (LJ14) 117 136
39: 312 type=190 (LJ14) 118 120
39: 313 type=190 (LJ14) 118 121
39: 314 type=190 (LJ14) 118 134
39: 315 type=191 (LJ14) 119 125
39: 316 type=192 (LJ14) 119 126
39: 317 type=192 (LJ14) 119 130
39: 318 type=190 (LJ14) 119 137
39: 319 type=192 (LJ14) 119 138
39: 320 type=193 (LJ14) 120 122
39: 321 type=193 (LJ14) 120 123
39: 322 type=191 (LJ14) 120 124
39: 323 type=194 (LJ14) 120 135
39: 324 type=186 (LJ14) 120 136
39: 325 type=191 (LJ14) 121 127
39: 326 type=191 (LJ14) 121 128
39: 327 type=191 (LJ14) 121 129
39: 328 type=191 (LJ14) 121 131
39: 329 type=191 (LJ14) 121 132
39: 330 type=191 (LJ14) 121 133
39: 331 type=195 (LJ14) 121 135
39: 332 type=187 (LJ14) 121 136
39: 333 type=193 (LJ14) 122 125
39: 334 type=191 (LJ14) 122 126
39: 335 type=191 (LJ14) 122 130
39: 336 type=196 (LJ14) 122 134
39: 337 type=193 (LJ14) 123 125
39: 338 type=191 (LJ14) 123 126
39: 339 type=191 (LJ14) 123 130
39: 340 type=196 (LJ14) 123 134
39: 341 type=197 (LJ14) 124 134
39: 342 type=193 (LJ14) 125 127
39: 343 type=193 (LJ14) 125 128
39: 344 type=193 (LJ14) 125 129
39: 345 type=193 (LJ14) 125 131
39: 346 type=193 (LJ14) 125 132
39: 347 type=193 (LJ14) 125 133
39: 348 type=191 (LJ14) 126 131
39: 349 type=191 (LJ14) 126 132
39: 350 type=191 (LJ14) 126 133
39: 351 type=191 (LJ14) 127 130
39: 352 type=191 (LJ14) 128 130
39: 353 type=191 (LJ14) 129 130
39: 354 type=196 (LJ14) 134 139
39: 355 type=197 (LJ14) 134 140
39: 356 type=198 (LJ14) 134 144
39: 357 type=190 (LJ14) 135 137
39: 358 type=195 (LJ14) 135 138
39: 359 type=186 (LJ14) 136 141
39: 360 type=186 (LJ14) 136 142
39: 361 type=186 (LJ14) 136 143
39: 362 type=188 (LJ14) 136 145
39: 363 type=189 (LJ14) 136 146
39: 364 type=190 (LJ14) 137 139
39: 365 type=190 (LJ14) 137 140
39: 366 type=190 (LJ14) 137 144
39: 367 type=190 (LJ14) 138 147
39: 368 type=192 (LJ14) 138 148
39: 369 type=193 (LJ14) 139 141
39: 370 type=193 (LJ14) 139 142
39: 371 type=193 (LJ14) 139 143
39: 372 type=194 (LJ14) 139 145
39: 373 type=186 (LJ14) 139 146
39: 374 type=195 (LJ14) 140 145
39: 375 type=187 (LJ14) 140 146
39: 376 type=196 (LJ14) 141 144
39: 377 type=196 (LJ14) 142 144
39: 378 type=196 (LJ14) 143 144
39: 379 type=196 (LJ14) 144 149
39: 380 type=197 (LJ14) 144 150
39: 381 type=198 (LJ14) 144 154
39: 382 type=190 (LJ14) 145 147
39: 383 type=195 (LJ14) 145 148
39: 384 type=186 (LJ14) 146 151
39: 385 type=186 (LJ14) 146 152
39: 386 type=186 (LJ14) 146 153
39: 387 type=188 (LJ14) 146 155
39: 388 type=190 (LJ14) 147 149
39: 389 type=190 (LJ14) 147 150
39: 390 type=190 (LJ14) 147 154
39: 391 type=193 (LJ14) 149 151
39: 392 type=193 (LJ14) 149 152
39: 393 type=193 (LJ14) 149 153
39: 394 type=194 (LJ14) 149 155
39: 395 type=195 (LJ14) 150 155
39: 396 type=196 (LJ14) 151 154
39: 397 type=196 (LJ14) 152 154
39: 398 type=196 (LJ14) 153 154
39: Coulomb-14:
39: nr: 0
39: LJC-14 q:
39: nr: 0
39: LJC Pairs NB:
39: nr: 0
39: LJ (SR):
39: nr: 0
39: Buck.ham (SR):
39: nr: 0
39: LJ (unused):
39: nr: 0
39: B.ham (unused):
39: nr: 0
39: Disper. corr.:
39: nr: 0
39: Coulomb (SR):
39: nr: 0
39: Coul (unused):
39: nr: 0
39: RF excl.:
39: nr: 0
39: Coul. recip.:
39: nr: 0
39: LJ recip.:
39: nr: 0
39: DPD:
39: nr: 0
39: Polarization:
39: nr: 0
39: Water Pol.:
39: nr: 0
39: Thole Pol.:
39: nr: 0
39: Anharm. Pol.:
39: nr: 0
39: Position Rest.:
39: nr: 0
39: Flat-bottom posres:
39: nr: 0
39: Dis. Rest.:
39: nr: 0
39: D.R.Viol. (nm):
39: nr: 0
39: Orient. Rest.:
39: nr: 0
39: Ori. R. RMSD:
39: nr: 0
39: Angle Rest.:
39: nr: 0
39: Angle Rest. Z:
39: nr: 0
39: Dih. Rest.:
39: nr: 0
39: Dih. Rest. Viol.:
39: nr: 0
39: Constraint:
39: nr: 0
39: Constr. No Conn.:
39: nr: 0
39: Settle:
39: nr: 0
39: Virtual site 2:
39: nr: 0
39: Virtual site 2fd:
39: nr: 0
39: Virtual site 3:
39: nr: 0
39: Virtual site 3fd:
39: nr: 0
39: Virtual site 3fad:
39: nr: 0
39: Virtual site 3out:
39: nr: 0
39: Virtual site 4fd:
39: nr: 0
39: Virtual site 4fdn:
39: nr: 0
39: Virtual site N:
39: nr: 0
39: COM Pull En.:
39: nr: 0
39: Density fitting:
39: nr: 0
39: Quantum En.:
39: nr: 0
39: Potential:
39: nr: 0
39: Kinetic En.:
39: nr: 0
39: Total Energy:
39: nr: 0
39: Conserved En.:
39: nr: 0
39: Temperature:
39: nr: 0
39: Vir. Temp. (not used):
39: nr: 0
39: Pres. DC:
39: nr: 0
39: Pressure:
39: nr: 0
39: dH/dl constr.:
39: nr: 0
39: dVremain/dl:
39: nr: 0
39: dEkin/dl:
39: nr: 0
39: dVcoul/dl:
39: nr: 0
39: dVvdw/dl:
39: nr: 0
39: dVbonded/dl:
39: nr: 0
39: dVrestraint/dl:
39: nr: 0
39: dVtemperature/dl:
39: nr: 0
39: grp[T-Coupling ] nr=1, name=[ rest]
39: grp[Energy Mon. ] nr=1, name=[ rest]
39: grp[Acceleration] nr=1, name=[ rest]
39: grp[Freeze ] nr=1, name=[ rest]
39: grp[User1 ] nr=1, name=[ rest]
39: grp[User2 ] nr=1, name=[ rest]
39: grp[VCM ] nr=1, name=[ rest]
39: grp[Compressed X] nr=1, name=[ rest]
39: grp[Or. Res. Fit] nr=1, name=[ rest]
39: grp[QMMM ] nr=1, name=[ rest]
39: grpname (11):
39: grpname[0]={name="System"}
39: grpname[1]={name="Protein"}
39: grpname[2]={name="Protein-H"}
39: grpname[3]={name="C-alpha"}
39: grpname[4]={name="Backbone"}
39: grpname[5]={name="MainChain"}
39: grpname[6]={name="MainChain+Cb"}
39: grpname[7]={name="MainChain+H"}
39: grpname[8]={name="SideChain"}
39: grpname[9]={name="SideChain-H"}
39: grpname[10]={name="rest"}
39: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM
39: allocated 0 0 0 0 0 0 0 0 0 0
39: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0
39: box (3x3):
39: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00}
39: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00}
39: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00}
39: box_rel (3x3):
39: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: boxv (3x3):
39: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: pres_prev (3x3):
39: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: svir_prev (3x3):
39: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: fvir_prev (3x3):
39: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: nosehoover_xi: not available
39: x (156x3):
39: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00}
39: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00}
39: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00}
39: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00}
39: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00}
39: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00}
39: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00}
39: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00}
39: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01}
39: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01}
39: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01}
39: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00}
39: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01}
39: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01}
39: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01}
39: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01}
39: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01}
39: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01}
39: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01}
39: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01}
39: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01}
39: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01}
39: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00}
39: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00}
39: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00}
39: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00}
39: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00}
39: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01}
39: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00}
39: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00}
39: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00}
39: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00}
39: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01}
39: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01}
39: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00}
39: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00}
39: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00}
39: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00}
39: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01}
39: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01}
39: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01}
39: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01}
39: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01}
39: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01}
39: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01}
39: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01}
39: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01}
39: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01}
39: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01}
39: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01}
39: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01}
39: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01}
39: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01}
39: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01}
39: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01}
39: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01}
39: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01}
39: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01}
39: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01}
39: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01}
39: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01}
39: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01}
39: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01}
39: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01}
39: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01}
39: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01}
39: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01}
39: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01}
39: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01}
39: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01}
39: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01}
39: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01}
39: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01}
39: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01}
39: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02}
39: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02}
39: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02}
39: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02}
39: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02}
39: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01}
39: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02}
39: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01}
39: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02}
39: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01}
39: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01}
39: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01}
39: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02}
39: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01}
39: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02}
39: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01}
39: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02}
39: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01}
39: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01}
39: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02}
39: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02}
39: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02}
39: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01}
39: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02}
39: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02}
39: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02}
39: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02}
39: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02}
39: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01}
39: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01}
39: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01}
39: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01}
39: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01}
39: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01}
39: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01}
39: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01}
39: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01}
39: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01}
39: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01}
39: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01}
39: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01}
39: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01}
39: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01}
39: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01}
39: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01}
39: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01}
39: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01}
39: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01}
39: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01}
39: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01}
39: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01}
39: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02}
39: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01}
39: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01}
39: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01}
39: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01}
39: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01}
39: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01}
39: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01}
39: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01}
39: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02}
39: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02}
39: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02}
39: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02}
39: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01}
39: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01}
39: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01}
39: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01}
39: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01}
39: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01}
39: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01}
39: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01}
39: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01}
39: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01}
39: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01}
39: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01}
39: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01}
39: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01}
39: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01}
39: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02}
39: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01}
39: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01}
39: v (156x3):
39: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: Group statistics
39: T-Coupling : 156 (total 156 atoms)
39: Energy Mon. : 156 (total 156 atoms)
39: Acceleration: 156 (total 156 atoms)
39: Freeze : 156 (total 156 atoms)
39: User1 : 156 (total 156 atoms)
39: User2 : 156 (total 156 atoms)
39: VCM : 156 (total 156 atoms)
39: Compressed X: 156 (total 156 atoms)
39: Or. Res. Fit: 156 (total 156 atoms)
39: QMMM : 156 (total 156 atoms)
39: [ OK ] DumpTest.WorksWithTpr (77 ms)
39: [ RUN ] DumpTest.WorksWithTprAndMdpWriting
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
39: [ OK ] DumpTest.WorksWithTprAndMdpWriting (3 ms)
39: [----------] 2 tests from DumpTest (80 ms total)
39:
39: [----------] 4 tests from ReportMethodsTest
39:
39: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
39: For a correct single-point energy evaluation with nsteps = 0, use
39: continuation = yes to avoid constraining the input coordinates.
39:
39: Setting the LD random seed to -1343234686
39: Generated 330891 of the 330891 non-bonded parameter combinations
39: Generating 1-4 interactions: fudge = 0.5
39: Generated 330891 of the 330891 1-4 parameter combinations
39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
39:
39: NOTE 2 [file lysozyme.top, line 1465]:
39: System has non-zero total charge: 2.000000
39: Total charge should normally be an integer. See
39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
39: for discussion on how close it should be to an integer.
39:
39:
39:
39: Number of degrees of freedom in T-Coupling group rest is 465.00
39:
39: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
39: NVE simulation with an initial temperature of zero: will use a Verlet
39: buffer of 10%. Check your energy drift!
39:
39:
39: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
39: You are using a plain Coulomb cut-off, which might produce artifacts.
39: You might want to consider using PME electrostatics.
39:
39:
39:
39: There were 4 notes
39: Analysing residue names:
39: There are: 10 Protein residues
39: Analysing Protein...
39: This run will generate roughly 0 Mb of data
39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
39: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms)
39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
39: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms)
39: [ RUN ] ReportMethodsTest.WritesCorrectInformation
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
39: [ OK ] ReportMethodsTest.WritesCorrectInformation (2 ms)
39: [ RUN ] ReportMethodsTest.ToolEndToEndTest
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
39: section: Methods
39: subsection: Simulation system
39: A system of 1 molecules (156 atoms) was simulated.
39:
39: subsection: Simulation settings
39: A total of 0 ns were simulated with a time step of 1 fs.
39: Neighbor searching was performed every 10 steps.
39: The Cut-off algorithm was used for electrostatic interactions.
39: with a cut-off of 1 nm.
39: A single cut-off of 1.1 nm was used for Van der Waals interactions.
39: [ OK ] ReportMethodsTest.ToolEndToEndTest (1 ms)
39: [----------] 4 tests from ReportMethodsTest (3 ms total)
39:
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: trr version: GMX_trn_file (single precision)
39:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (6 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (7 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (5 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from gro file '', 6 atoms.
39:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (6 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
39: -> frame 0 time 0.000
't= 0.00000', 6 atoms
39:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (5 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (5 ms)
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (34 ms total)
39:
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (2 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (3 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (2 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from gro file '', 6 atoms.
39:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (2 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
39: -> frame 0 time 0.000
't= 0.00000', 6 atoms
39:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (2 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (2 ms)
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (14 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 18 tests from 4 test cases ran. (2452 ms total)
39: [ PASSED ] 18 tests.
39/54 Test #39: ToolUnitTests ....................... Passed 2.48 sec
test 40
Start 40: FileIOTests
40: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/FileIOTests.xml"
40: Test timeout computed to be: 30
40: [==========] Running 33 tests from 8 test cases.
40: [----------] Global test environment set-up.
40: [----------] 2 tests from FileMD5Test
40: [ RUN ] FileMD5Test.CanComputeMD5
40: [ OK ] FileMD5Test.CanComputeMD5 (1 ms)
40: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
40: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms)
40: [----------] 2 tests from FileMD5Test (2 ms total)
40:
40: [----------] 3 tests from MrcSerializer
40: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet
40: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms)
40: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize
40: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms)
40: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip
40: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (5 ms)
40: [----------] 3 tests from MrcSerializer (5 ms total)
40:
40: [----------] 4 tests from MrcDensityMap
40: [ RUN ] MrcDensityMap.RoundTripIsIdempotent
40: [ OK ] MrcDensityMap.RoundTripIsIdempotent (6 ms)
40: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent
40: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms)
40: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile
40: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms)
40: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile
40: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (2 ms)
40: [----------] 4 tests from MrcDensityMap (9 ms total)
40:
40: [----------] 8 tests from MrcDensityMapHeaderTest
40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader
40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect
40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid
40: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.IsSane
40: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms)
40: [----------] 8 tests from MrcDensityMapHeaderTest (0 ms total)
40:
40: [----------] 9 tests from ReadTest
40: [ RUN ] ReadTest.get_eint_ReadsInteger
40: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
40: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side '0.8' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms)
40: [ RUN ] ReadTest.get_eint_WarnsAboutString
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side 'hello' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
40: [ RUN ] ReadTest.get_eint64_ReadsInteger
40: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
40: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side '0.8' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms)
40: [ RUN ] ReadTest.get_eint64_WarnsAboutString
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side 'hello' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
40: [ RUN ] ReadTest.get_ereal_ReadsInteger
40: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
40: [ RUN ] ReadTest.get_ereal_ReadsFloat
40: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
40: [ RUN ] ReadTest.get_ereal_WarnsAboutString
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side 'hello' for parameter 'test' in parameter file is not a
40: real value
40:
40:
40: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
40: [----------] 9 tests from ReadTest (1 ms total)
40:
40: [----------] 1 test from FileIOXdrSerializerTest
40: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect
40: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (0 ms)
40: [----------] 1 test from FileIOXdrSerializerTest (0 ms total)
40:
40: [----------] 2 tests from TngTest
40: [ RUN ] TngTest.CanOpenTngFile
40: TNG library: Cannot open file spc2-traj.tng. /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: 890
40: TNG library: Cannot open file spc2-traj.tng. /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: 890
40: [ OK ] TngTest.CanOpenTngFile (0 ms)
40: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
40: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
40: [----------] 2 tests from TngTest (1 ms total)
40:
40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (1 ms)
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms)
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (5 ms)
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms)
40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (8 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 33 tests from 8 test cases ran. (26 ms total)
40: [ PASSED ] 33 tests.
40/54 Test #40: FileIOTests ......................... Passed 0.05 sec
test 41
Start 41: SelectionUnitTests
41: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml"
41: Test timeout computed to be: 30
41: [==========] Running 192 tests from 11 test cases.
41: [----------] Global test environment set-up.
41: [----------] 1 test from IndexGroupTest
41: [ RUN ] IndexGroupTest.RemovesDuplicates
41: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
41: [----------] 1 test from IndexGroupTest (0 ms total)
41:
41: [----------] 15 tests from IndexBlockTest
41: [ RUN ] IndexBlockTest.CreatesUnknownBlock
41: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms)
41: [ RUN ] IndexBlockTest.CreatesAtomBlock
41: [ OK ] IndexBlockTest.CreatesAtomBlock (1 ms)
41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology
41: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (0 ms)
41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology
41: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (1 ms)
41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology
41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms)
41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology
41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (0 ms)
41: [ RUN ] IndexBlockTest.CreatesSingleBlock
41: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
41: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms)
41: [----------] 15 tests from IndexBlockTest (4 ms total)
41:
41: [----------] 11 tests from IndexMapTest
41: [ RUN ] IndexMapTest.InitializesAtomBlock
41: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
41: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
41: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (1 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
41: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
41: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
41: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (1 ms)
41: [ RUN ] IndexMapTest.InitializesMoleculeBlock
41: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms)
41: [ RUN ] IndexMapTest.MapsSingleBlock
41: [ OK ] IndexMapTest.MapsSingleBlock (0 ms)
41: [ RUN ] IndexMapTest.MapsResidueBlocks
41: [ OK ] IndexMapTest.MapsResidueBlocks (1 ms)
41: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
41: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (1 ms)
41: [ RUN ] IndexMapTest.HandlesMultipleRequests
41: [ OK ] IndexMapTest.HandlesMultipleRequests (1 ms)
41: [----------] 11 tests from IndexMapTest (5 ms total)
41:
41: [----------] 3 tests from IndexGroupsAndNamesTest
41: [ RUN ] IndexGroupsAndNamesTest.containsNames
41: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms)
41: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing
41: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms)
41: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect
41: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms)
41: [----------] 3 tests from IndexGroupsAndNamesTest (0 ms total)
41:
41: [----------] 15 tests from NeighborhoodSearchTest
41: [ RUN ] NeighborhoodSearchTest.SimpleSearch
41: [ OK ] NeighborhoodSearchTest.SimpleSearch (35 ms)
41: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
41: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (35 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchBox
41: [ OK ] NeighborhoodSearchTest.GridSearchBox (5 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
41: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (21 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
41: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (11 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
41: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (5 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
41: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (5 ms)
41: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
41: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
41: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (101 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
41: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
41: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
41: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
41: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms)
41: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
41: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (8 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
41: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (2 ms)
41: [----------] 15 tests from NeighborhoodSearchTest (230 ms total)
41:
41: [----------] 12 tests from PositionCalculationTest
41: [ RUN ] PositionCalculationTest.ComputesAtomPositions
41: [ OK ] PositionCalculationTest.ComputesAtomPositions (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
41: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms)
41: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
41: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
41: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms)
41: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
41: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms)
41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesPositionMask
41: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms)
41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (1 ms)
41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms)
41: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
41: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (1 ms)
41: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
41: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms)
41: [----------] 12 tests from PositionCalculationTest (6 ms total)
41:
41: [----------] 29 tests from SelectionCollectionTest
41: [ RUN ] SelectionCollectionTest.HandlesNoSelections
41: [ OK ] SelectionCollectionTest.HandlesNoSelections (0 ms)
41: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
41: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
41: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
41: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (1 ms)
41: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
41: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
41: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
41: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
41: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
41: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (2 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
41: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (2 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (3 ms)
41: [----------] 29 tests from SelectionCollectionTest (37 ms total)
41:
41: [----------] 14 tests from SelectionCollectionInteractiveTest
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
41: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
41: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (1 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms)
41: [----------] 14 tests from SelectionCollectionInteractiveTest (24 ms total)
41:
41: [----------] 66 tests from SelectionCollectionDataTest
41: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
41: [ OK ] SelectionCollectionDataTest.HandlesAllNone (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
41: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesResnr
41: [ OK ] SelectionCollectionDataTest.HandlesResnr (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
41: [ OK ] SelectionCollectionDataTest.HandlesResIndex (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
41: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
41: [ OK ] SelectionCollectionDataTest.HandlesAtomname (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
41: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
41: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesChain
41: [ OK ] SelectionCollectionDataTest.HandlesChain (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMass
41: [ OK ] SelectionCollectionDataTest.HandlesMass (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesCharge
41: [ OK ] SelectionCollectionDataTest.HandlesCharge (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
41: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
41: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
41: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBeta
41: [ OK ] SelectionCollectionDataTest.HandlesBeta (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesResname
41: [ OK ] SelectionCollectionDataTest.HandlesResname (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
41: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
41: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
41: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
41: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (16 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
41: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
41: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (13 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
41: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (14 ms)
41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (6 ms)
41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
41: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
41: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (1 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
41: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
41: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
41: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
41: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
41: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (10 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
41: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
41: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
41: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
41: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
41: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
41: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
41: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (10 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (7 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
41: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (13 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (7 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
41: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (6 ms)
41: [----------] 66 tests from SelectionCollectionDataTest (327 ms total)
41:
41: [----------] 17 tests from SelectionOptionTest
41: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
41: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms)
41: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
41: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
41: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (2 ms)
41: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
41: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (2 ms)
41: [ RUN ] SelectionOptionTest.ChecksEmptySelections
41: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms)
41: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
41: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooManySelections
41: [ OK ] SelectionOptionTest.HandlesTooManySelections (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
41: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms)
41: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
41: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesAdjuster
41: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
41: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
41: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms)
41: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
41: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms)
41: [----------] 17 tests from SelectionOptionTest (15 ms total)
41:
41: [----------] 9 tests from SelectionFileOptionTest
41: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
41: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
41: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
41: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
41: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
41: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms)
41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
41: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
41: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (1 ms)
41: [----------] 9 tests from SelectionFileOptionTest (7 ms total)
41:
41: [----------] Global test environment tear-down
41: [==========] 192 tests from 11 test cases ran. (656 ms total)
41: [ PASSED ] 192 tests.
41/54 Test #41: SelectionUnitTests .................. Passed 0.69 sec
test 42
Start 42: MdrunOutputTests
42: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml"
42: Test timeout computed to be: 600
42: [==========] Running 12 tests from 5 test cases.
42: [----------] Global test environment set-up.
42: [----------] 1 test from MdrunTest
42: [ RUN ] MdrunTest.WritesHelp
42: [ OK ] MdrunTest.WritesHelp (5 ms)
42: [----------] 1 test from MdrunTest (5 ms total)
42:
42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
42: Setting the LD random seed to 1659636518
42: Generated 3 of the 3 non-bonded parameter combinations
42: Generating 1-4 interactions: fudge = 0.5
42: Generated 3 of the 3 1-4 parameter combinations
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group rest is 9.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
42: NVE simulation: will use the initial temperature of 2573.591 K for
42: determining the Verlet buffer size
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There were 2 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc2'
42: 1 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.180 0.090 199.3
42: (ns/day) (hour/ns)
42: Performance: 1.911 12.556
42:
Reading frame 0 time 0.000
42: # Atoms 6
42:
Reading frame 1 time 0.001
Last frame 1 time 0.001
42:
42:
42: Item #frames Timestep (ps)
42: Step 2 0.001
42: Time 2 0.001
42: Lambda 0
42: Coords 2 0.001
42: Velocities 0
42: Forces 0
42: Box 2 0.001
42: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (133 ms)
42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
42: Setting the LD random seed to -1324217851
42: Generated 3 of the 3 non-bonded parameter combinations
42: Generating 1-4 interactions: fudge = 0.5
42: Generated 3 of the 3 1-4 parameter combinations
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group rest is 9.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
42: NVE simulation: will use the initial temperature of 2573.591 K for
42: determining the Verlet buffer size
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There were 2 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc2'
42: 1 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.154 0.077 199.2
42: (ns/day) (hour/ns)
42: Performance: 2.231 10.755
42:
Reading frame 0 time 0.000
42: # Atoms 6
42:
Reading frame 1 time 0.001
Last frame 1 time 0.001
42:
42:
42: Item #frames Timestep (ps)
42: Step 2 0.001
42: Time 2 0.001
42: Lambda 0
42: Coords 2 0.001
42: Velocities 0
42: Forces 0
42: Box 2 0.001
42: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (100 ms)
42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
42: Setting the LD random seed to -464449059
42: Generated 3 of the 3 non-bonded parameter combinations
42: Generating 1-4 interactions: fudge = 0.5
42: Generated 3 of the 3 1-4 parameter combinations
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group rest is 9.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
42: NVE simulation: will use the initial temperature of 2573.591 K for
42: determining the Verlet buffer size
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There were 2 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc2'
42: 1 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.139 0.070 199.1
42: (ns/day) (hour/ns)
42: Performance: 2.483 9.666
42:
Reading frame 0 time 0.000
42: # Atoms 3
42:
Reading frame 1 time 0.001
Last frame 1 time 0.001
42:
42:
42: Item #frames Timestep (ps)
42: Step 2 0.001
42: Time 2 0.001
42: Lambda 0
42: Coords 2 0.001
42: Velocities 0
42: Forces 0
42: Box 2 0.001
42: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (91 ms)
42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (325 ms total)
42:
42: [----------] 2 tests from Argon12/OutputFiles
42: [ RUN ] Argon12/OutputFiles.FilesArePresent/0
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
42: that with the Verlet scheme, nstlist has no effect on the accuracy of
42: your simulation.
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
42: Setting nstcalcenergy (100) equal to nstenergy (4)
42:
42: Generated 1 of the 1 non-bonded parameter combinations
42: Excluding 1 bonded neighbours molecule type 'Argon'
42: Number of degrees of freedom in T-Coupling group System is 33.00
42:
42: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
42: NVE simulation: will use the initial temperature of 68.810 K for
42: determining the Verlet buffer size
42:
42:
42: There were 3 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'Argon'
42: 16 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.190 0.095 199.4
42: (ns/day) (hour/ns)
42: Performance: 15.451 1.553
42: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (116 ms)
42: [ RUN ] Argon12/OutputFiles.FilesArePresent/1
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
42: that with the Verlet scheme, nstlist has no effect on the accuracy of
42: your simulation.
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
42: Setting nstcalcenergy (100) equal to nstenergy (4)
42:
42: Generated 1 of the 1 non-bonded parameter combinations
42: Excluding 1 bonded neighbours molecule type 'Argon'
42: Number of degrees of freedom in T-Coupling group System is 33.00
42:
42: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
42: NVE simulation: will use the initial temperature of 68.810 K for
42: determining the Verlet buffer size
42:
42:
42: There were 3 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'Argon'
42: 16 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.192 0.096 199.6
42: (ns/day) (hour/ns)
42: Performance: 15.270 1.572
42: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (117 ms)
42: [----------] 2 tests from Argon12/OutputFiles (233 ms total)
42:
42: [----------] 3 tests from MdrunCanWrite/Trajectories
42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
42: Setting the LD random seed to -1893294519
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 6 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.132 0.066 199.0
42: (ns/day) (hour/ns)
42: Performance: 9.111 2.634
42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (92 ms)
42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
42: Setting the LD random seed to 362171610
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 6 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.131 0.066 199.0
42: (ns/day) (hour/ns)
42: Performance: 9.204 2.608
42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (92 ms)
42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
42: Setting the LD random seed to -837809468
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 6 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.148 0.074 199.1
42: (ns/day) (hour/ns)
42: Performance: 8.152 2.944
42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (100 ms)
42: [----------] 3 tests from MdrunCanWrite/Trajectories (284 ms total)
42:
42: [----------] 3 tests from MdrunCanWrite/NptTrajectories
42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
42: Setting the LD random seed to -1417032317
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 2 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.133 0.067 199.0
42: (ns/day) (hour/ns)
42: Performance: 3.889 6.171
42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (91 ms)
42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
42: Setting the LD random seed to -472214545
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 2 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.116 0.059 198.8
42: (ns/day) (hour/ns)
42: Performance: 4.428 5.421
42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (84 ms)
42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
42: Setting the LD random seed to 853248495
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 2 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.116 0.059 198.6
42: (ns/day) (hour/ns)
42: Performance: 4.430 5.417
42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (83 ms)
42: [----------] 3 tests from MdrunCanWrite/NptTrajectories (258 ms total)
42:
42: [----------] Global test environment tear-down
42: [==========] 12 tests from 5 test cases ran. (1105 ms total)
42: [ PASSED ] 12 tests.
42/54 Test #42: MdrunOutputTests .................... Passed 1.13 sec
test 43
Start 43: MdrunModulesTests
43: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml"
43: Test timeout computed to be: 600
43: [==========] Running 10 tests from 3 test cases.
43: [----------] Global test environment set-up.
43: [----------] 4 tests from DensityFittingTest
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct
43: Setting the LD random seed to -1945011533
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -3.85654101644806e+03
43: Maximum force = 2.88468568366558e+03 on atom 3
43: Norm of force = 1.07544474716821e+03
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (46 ms)
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy
43: Setting the LD random seed to -573337747
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -2.71386626596691e+04
43: Maximum force = 4.34097106676756e+03 on atom 2
43: Norm of force = 1.25497916295893e+03
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (26 ms)
43: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch
43:
43: [WARNING] /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-death-test.cc:836:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads.
43: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (18 ms)
43: [ RUN ] DensityFittingTest.CheckpointWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (2)
43:
43: Setting the LD random seed to -1222879489
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.127 0.064 199.2
43: (ns/day) (hour/ns)
43: Performance: 4.051 5.925
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
43: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps
43: Can not increase nstlist because an NVE ensemble is used
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.114 0.057 199.1
43: (ns/day) (hour/ns)
43: Performance: 7.574 3.169
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (154 ms)
43: [----------] 4 tests from DensityFittingTest (244 ms total)
43:
43: [----------] 4 tests from MimicTest
43: [ RUN ] MimicTest.OneQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 1418251611
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.002 0.001 175.7
43: (ns/day) (hour/ns)
43: Performance: 96.099 0.250
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.OneQuantumMol (22 ms)
43: [ RUN ] MimicTest.AllQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 1434340347
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.002 0.001 175.2
43: (ns/day) (hour/ns)
43: Performance: 98.368 0.244
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.AllQuantumMol (23 ms)
43: [ RUN ] MimicTest.TwoQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 307038082
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.002 0.001 174.9
43: (ns/day) (hour/ns)
43: Performance: 99.040 0.242
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.TwoQuantumMol (22 ms)
43: [ RUN ] MimicTest.BondCuts
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1508519343
43: Generated 2211 of the 2211 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2211 of the 2211 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
43: Number of degrees of freedom in T-Coupling group rest is 66.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: NVE simulation: will use the initial temperature of 300.368 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
43:
43: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.001 183.7
43: (ns/day) (hour/ns)
43: Performance: 58.858 0.408
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
43: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.BondCuts (72 ms)
43: [----------] 4 tests from MimicTest (139 ms total)
43:
43: [----------] 2 tests from WithIntegrator/ImdTest
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0
43: Setting the LD random seed to -855886806
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43:
43: NOTE 1 [file glycine_vacuo.top, line 12]:
43: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an
43: estimated oscillational period of 1.0e-02 ps, which is less than 10 times
43: the time step of 2.0e-03 ps.
43: Maybe you forgot to change the constraints mdp option.
43:
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
43: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 36011.
43: IMD: -imdwait not set, starting simulation.
43: starting mdrun 'Glycine'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.124 0.063 198.8
43: (ns/day) (hour/ns)
43: Performance: 8.281 2.898
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (518 ms)
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not
43: apply to steep.
43:
43: Setting the LD random seed to 1712027205
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 47999.
43: IMD: -imdwait not set, starting simulation.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = 1.19770464690297e+03
43: Maximum force = 1.77948604657896e+04 on atom 9
43: Norm of force = 7.87328617833980e+03
43: This run will generate roughly 0 Mb of data
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (457 ms)
43: [----------] 2 tests from WithIntegrator/ImdTest (975 ms total)
43:
43: [----------] Global test environment tear-down
43: [==========] 10 tests from 3 test cases ran. (1358 ms total)
43: [ PASSED ] 10 tests.
43/54 Test #43: MdrunModulesTests ................... Passed 1.38 sec
test 44
Start 44: MdrunIOTests
44: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunIOTests.xml"
44: Test timeout computed to be: 600
44: [==========] Running 51 tests from 9 test cases.
44: [----------] Global test environment set-up.
44: [----------] 3 tests from GromppTest
44: [ RUN ] GromppTest.EmptyMdpFileWorks
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
44: For a correct single-point energy evaluation with nsteps = 0, use
44: continuation = yes to avoid constraining the input coordinates.
44:
44: Setting the LD random seed to -1763522028
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 12.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
44: NVE simulation: will use the initial temperature of 1046.791 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: [ OK ] GromppTest.EmptyMdpFileWorks (10 ms)
44: [ RUN ] GromppTest.SimulatedAnnealingWorks
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
44: For a correct single-point energy evaluation with nsteps = 0, use
44: continuation = yes to avoid constraining the input coordinates.
44:
44: Setting the LD random seed to -1329337956
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Simulated annealing for group rest: Periodic, 4 timepoints
44: Time (ps) Temperature (K)
44: 0.0 298.0
44: 2.0 320.0
44: 4.0 320.0
44: 6.0 298.0
44: Number of degrees of freedom in T-Coupling group rest is 12.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
44: NVE simulation: will use the initial temperature of 1046.791 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: [ OK ] GromppTest.SimulatedAnnealingWorks (10 ms)
44: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
44: For a correct single-point energy evaluation with nsteps = 0, use
44: continuation = yes to avoid constraining the input coordinates.
44:
44: Setting the LD random seed to 785816070
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Simulated annealing for group Methanol: Single, 3 timepoints
44: Time (ps) Temperature (K)
44: 0.0 298.0
44: 3.0 280.0
44: 6.0- 270.0
44: Simulated annealing for group SOL: Periodic, 4 timepoints
44: Time (ps) Temperature (K)
44: 0.0 298.0
44: 2.0 320.0
44: 4.0 320.0
44: 6.0 298.0
44: Number of degrees of freedom in T-Coupling group Methanol is 7.20
44: Number of degrees of freedom in T-Coupling group SOL is 4.80
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
44: NVE simulation: will use the initial temperature of 1046.791 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (9 ms)
44: [----------] 3 tests from GromppTest (29 ms total)
44:
44: [----------] 6 tests from MdrunTerminationTest
44: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault
44: Setting the LD random seed to -1079654375
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.142 0.071 199.2
44: (ns/day) (hour/ns)
44: Performance: 3.643 6.588
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.128 0.064 199.1
44: (ns/day) (hour/ns)
44: Performance: 4.025 5.962
44: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (189 ms)
44: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
44: Setting the LD random seed to 1743106226
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 10 to 1, rlist from 1.024 to 1
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 100 steps, 0.1 ps.
44:
44: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.118 0.060 199.1
44: (ns/day) (hour/ns)
44: Performance: 4.356 5.510
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Setting nsteps to 102
44: Writing statusfile with starting step 0 and length 102 steps...
44: time 0.000 and length 0.102 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 102 steps, 0.1 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.130 0.065 199.2
44: (ns/day) (hour/ns)
44: Performance: 134.067 0.179
44: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (159 ms)
44: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend
44: Setting the LD random seed to 60231920
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.135 0.068 199.2
44: (ns/day) (hour/ns)
44: Performance: 3.819 6.285
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.111 0.056 199.4
44: (ns/day) (hour/ns)
44: Performance: 4.640 5.172
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Setting nsteps to 6
44: Writing statusfile with starting step 0 and length 6 steps...
44: time 0.000 and length 0.006 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.123 0.062 199.5
44: (ns/day) (hour/ns)
44: Performance: 4.203 5.710
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Setting nsteps to 8
44: Writing statusfile with starting step 0 and length 8 steps...
44: time 0.000 and length 0.008 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.125 0.063 199.5
44: (ns/day) (hour/ns)
44: Performance: 4.126 5.817
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.001 0.001 162.7
44: (ns/day) (hour/ns)
44: Performance: 100.944 0.238
44: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (318 ms)
44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile
44: Setting the LD random seed to -15603022
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.114 0.057 199.0
44: (ns/day) (hour/ns)
44: Performance: 4.538 5.288
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.127 0.064 199.0
44: (ns/day) (hour/ns)
44: Performance: 6.777 3.541
44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (156 ms)
44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile
44: Setting the LD random seed to -1106632572
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.136 0.068 199.2
44: (ns/day) (hour/ns)
44: Performance: 3.802 6.313
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (94 ms)
44: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles
44: Setting the LD random seed to 1394976911
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.132 0.067 199.1
44: (ns/day) (hour/ns)
44: Performance: 3.895 6.161
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.128 0.064 199.5
44: (ns/day) (hour/ns)
44: Performance: 4.041 5.940
44: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (163 ms)
44: [----------] 6 tests from MdrunTerminationTest (1079 ms total)
44:
44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.166 0.083 199.4
44: (ns/day) (hour/ns)
44: Performance: 17.678 1.358
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.168 0.084 199.3
44: (ns/day) (hour/ns)
44: Performance: 9.249 2.595
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.182 0.091 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.529 2.814
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (315 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.188 0.094 199.6
44: (ns/day) (hour/ns)
44: Performance: 15.578 1.541
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.152 0.076 199.5
44: (ns/day) (hour/ns)
44: Performance: 10.189 2.356
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.183 0.092 199.6
44: (ns/day) (hour/ns)
44: Performance: 8.472 2.833
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (317 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.202 0.101 199.5
44: (ns/day) (hour/ns)
44: Performance: 14.485 1.657
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.201 0.101 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.724 3.107
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.5
44: (ns/day) (hour/ns)
44: Performance: 7.219 3.324
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (366 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.186 0.093 199.4
44: (ns/day) (hour/ns)
44: Performance: 15.720 1.527
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.201 0.101 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.723 3.108
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.182 0.091 199.4
44: (ns/day) (hour/ns)
44: Performance: 8.540 2.810
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (342 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.200 0.100 199.4
44: (ns/day) (hour/ns)
44: Performance: 14.673 1.636
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.167 0.084 199.2
44: (ns/day) (hour/ns)
44: Performance: 9.277 2.587
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.165 0.083 199.3
44: (ns/day) (hour/ns)
44: Performance: 9.370 2.561
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (325 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.169 0.085 199.5
44: (ns/day) (hour/ns)
44: Performance: 17.363 1.382
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.185 0.093 199.6
44: (ns/day) (hour/ns)
44: Performance: 8.375 2.866
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.183 0.092 199.5
44: (ns/day) (hour/ns)
44: Performance: 8.457 2.838
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (325 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.5
44: (ns/day) (hour/ns)
44: Performance: 13.640 1.760
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.166 0.083 199.1
44: (ns/day) (hour/ns)
44: Performance: 9.317 2.576
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.164 0.082 199.2
44: (ns/day) (hour/ns)
44: Performance: 9.443 2.542
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (333 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.183 0.092 199.4
44: (ns/day) (hour/ns)
44: Performance: 16.032 1.497
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.167 0.084 199.2
44: (ns/day) (hour/ns)
44: Performance: 9.299 2.581
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.164 0.082 199.3
44: (ns/day) (hour/ns)
44: Performance: 9.432 2.545
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (317 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.241 0.121 199.4
44: (ns/day) (hour/ns)
44: Performance: 12.155 1.975
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.174 0.088 199.1
44: (ns/day) (hour/ns)
44: Performance: 8.877 2.704
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.188 0.095 199.2
44: (ns/day) (hour/ns)
44: Performance: 8.226 2.918
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (469 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.236 0.118 199.4
44: (ns/day) (hour/ns)
44: Performance: 12.410 1.934
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.191 0.096 199.2
44: (ns/day) (hour/ns)
44: Performance: 8.096 2.964
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.187 0.094 199.2
44: (ns/day) (hour/ns)
44: Performance: 8.262 2.905
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (475 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.218 0.109 199.3
44: (ns/day) (hour/ns)
44: Performance: 13.447 1.785
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.207 0.104 199.2
44: (ns/day) (hour/ns)
44: Performance: 7.499 3.200
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.187 0.094 199.2
44: (ns/day) (hour/ns)
44: Performance: 8.302 2.891
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (550 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.268 0.135 199.4
44: (ns/day) (hour/ns)
44: Performance: 10.917 2.198
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.207 0.104 199.2
44: (ns/day) (hour/ns)
44: Performance: 7.496 3.202
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.221 0.111 199.2
44: (ns/day) (hour/ns)
44: Performance: 7.023 3.417
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (567 ms)
44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (4701 ms total)
44:
44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.237 0.119 199.2
44: (ns/day) (hour/ns)
44: Performance: 12.342 1.945
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.256 0.129 199.1
44: (ns/day) (hour/ns)
44: Performance: 6.049 3.968
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.252 0.126 199.3
44: (ns/day) (hour/ns)
44: Performance: 6.151 3.902
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (542 ms)
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.289 0.145 199.6
44: (ns/day) (hour/ns)
44: Performance: 10.158 2.363
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.258 0.129 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.014 3.991
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.220 0.110 199.5
44: (ns/day) (hour/ns)
44: Performance: 7.039 3.410
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (550 ms)
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.222 0.112 199.2
44: (ns/day) (hour/ns)
44: Performance: 13.147 1.825
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.230 0.115 199.1
44: (ns/day) (hour/ns)
44: Performance: 6.744 3.559
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.259 0.130 199.2
44: (ns/day) (hour/ns)
44: Performance: 5.988 4.008
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (616 ms)
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.265 0.133 199.3
44: (ns/day) (hour/ns)
44: Performance: 11.030 2.176
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.236 0.118 199.1
44: (ns/day) (hour/ns)
44: Performance: 6.571 3.652
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.214 0.107 199.1
44: (ns/day) (hour/ns)
44: Performance: 7.248 3.311
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (583 ms)
44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (2292 ms total)
44:
44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.144 0.072 199.2
44: (ns/day) (hour/ns)
44: Performance: 20.338 1.180
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.135 3.363
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.182 0.091 199.4
44: (ns/day) (hour/ns)
44: Performance: 8.535 2.812
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (330 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.203 0.102 199.5
44: (ns/day) (hour/ns)
44: Performance: 14.454 1.660
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.184 0.092 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.423 2.850
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.181 0.091 199.4
44: (ns/day) (hour/ns)
44: Performance: 8.543 2.809
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (341 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.169 0.085 199.4
44: (ns/day) (hour/ns)
44: Performance: 17.284 1.389
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.201 0.101 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.714 3.111
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.215 0.108 199.5
44: (ns/day) (hour/ns)
44: Performance: 7.215 3.326
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (350 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.186 0.093 199.3
44: (ns/day) (hour/ns)
44: Performance: 15.725 1.526
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.167 0.084 199.3
44: (ns/day) (hour/ns)
44: Performance: 9.258 2.592
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.198 0.099 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.846 3.059
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (333 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.155 0.078 199.5
44: (ns/day) (hour/ns)
44: Performance: 18.909 1.269
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.169 0.085 199.5
44: (ns/day) (hour/ns)
44: Performance: 9.177 2.615
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.183 0.091 199.5
44: (ns/day) (hour/ns)
44: Performance: 8.501 2.823
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (309 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.186 0.093 199.4
44: (ns/day) (hour/ns)
44: Performance: 15.776 1.521
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.184 0.092 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.411 2.854
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.231 0.116 199.5
44: (ns/day) (hour/ns)
44: Performance: 6.720 3.571
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (358 ms)
44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (2021 ms total)
44:
44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.169 0.085 199.3
44: (ns/day) (hour/ns)
44: Performance: 17.298 1.387
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.151 0.076 199.1
44: (ns/day) (hour/ns)
44: Performance: 10.268 2.337
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.165 0.083 199.3
44: (ns/day) (hour/ns)
44: Performance: 9.412 2.550
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (301 ms)
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.201 0.101 199.4
44: (ns/day) (hour/ns)
44: Performance: 14.561 1.648
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.201 0.101 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.721 3.109
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.198 0.099 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.838 3.062
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (359 ms)
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.183 0.092 199.3
44: (ns/day) (hour/ns)
44: Performance: 15.963 1.503
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.168 0.084 199.2
44: (ns/day) (hour/ns)
44: Performance: 9.245 2.596
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.164 0.083 199.3
44: (ns/day) (hour/ns)
44: Performance: 9.425 2.546
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (316 ms)
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.219 0.110 199.6
44: (ns/day) (hour/ns)
44: Performance: 13.365 1.796
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.186 0.093 199.5
44: (ns/day) (hour/ns)
44: Performance: 8.342 2.877
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.199 0.100 199.6
44: (ns/day) (hour/ns)
44: Performance: 7.782 3.084
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (359 ms)
44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (1335 ms total)
44:
44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.182 0.091 199.3
44: (ns/day) (hour/ns)
44: Performance: 16.068 1.494
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.151 0.076 199.1
44: (ns/day) (hour/ns)
44: Performance: 10.284 2.334
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.164 0.083 199.2
44: (ns/day) (hour/ns)
44: Performance: 9.419 2.548
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (307 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.151 0.076 199.2
44: (ns/day) (hour/ns)
44: Performance: 19.424 1.236
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.150 0.076 199.0
44: (ns/day) (hour/ns)
44: Performance: 10.291 2.332
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.214 0.107 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.245 3.313
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (317 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.200 0.100 199.4
44: (ns/day) (hour/ns)
44: Performance: 14.678 1.635
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.200 0.101 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.733 3.104
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.181 0.091 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.568 2.801
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (349 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.217 0.109 199.4
44: (ns/day) (hour/ns)
44: Performance: 13.470 1.782
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.184 0.092 199.2
44: (ns/day) (hour/ns)
44: Performance: 8.425 2.849
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.180 0.091 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.588 2.795
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (351 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Using Berendsen pressure coupling invalidates the true ensemble for the
44: thermostat
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: There was 1 warning
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Using Berendsen pressure coupling invalidates the true ensemble for the
44: thermostat
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: There was 1 warning
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.182 0.092 199.3
44: (ns/day) (hour/ns)
44: Performance: 16.050 1.495
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.184 0.092 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.425 2.849
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.181 0.091 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.557 2.805
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (332 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.201 0.101 199.4
44: (ns/day) (hour/ns)
44: Performance: 14.592 1.645
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.184 0.092 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.426 2.848
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.181 0.091 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.574 2.799
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (342 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.200 0.100 199.4
44: (ns/day) (hour/ns)
44: Performance: 14.674 1.636
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.184 0.092 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.415 2.852
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.214 0.107 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.252 3.309
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (358 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7
44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (0 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.200 0.100 199.4
44: (ns/day) (hour/ns)
44: Performance: 14.625 1.641
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.184 0.092 199.3
44: (ns/day) (hour/ns)
44: Performance: 8.420 2.850
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.164 0.082 199.2
44: (ns/day) (hour/ns)
44: Performance: 9.448 2.540
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (333 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.170 0.085 199.5
44: (ns/day) (hour/ns)
44: Performance: 17.262 1.390
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.152 0.076 199.4
44: (ns/day) (hour/ns)
44: Performance: 10.187 2.356
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.149 0.075 199.4
44: (ns/day) (hour/ns)
44: Performance: 10.393 2.309
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (292 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10
44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (0 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11
44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (0 ms)
44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact (2983 ms total)
44:
44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact
44: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.232 0.116 199.4
44: (ns/day) (hour/ns)
44: Performance: 12.637 1.899
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.200 0.101 199.3
44: (ns/day) (hour/ns)
44: Performance: 7.732 3.104
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.196 0.099 199.4
44: (ns/day) (hour/ns)
44: Performance: 7.894 3.040
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (375 ms)
44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (375 ms total)
44:
44: [----------] 3 tests from Checking/InitialConstraintsTest
44: [ RUN ] Checking/InitialConstraintsTest.Works/0
44: Setting the LD random seed to -1761987196
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 11.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 1141.954 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc-and-methanol'
44: 1 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.120 0.060 198.9
44: (ns/day) (hour/ns)
44: Performance: 2.859 8.395
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (85 ms)
44: [ RUN ] Checking/InitialConstraintsTest.Works/1
44: Setting the LD random seed to 461746428
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 11.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 1141.954 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc-and-methanol'
44: 1 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.102 0.051 198.9
44: (ns/day) (hour/ns)
44: Performance: 3.362 7.138
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (75 ms)
44: [ RUN ] Checking/InitialConstraintsTest.Works/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
44: Integrator method md-vv-avek is implemented primarily for validation
44: purposes; for molecular dynamics, you should probably be using md or md-vv
44:
44: Setting the LD random seed to 596398654
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 11.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 1141.954 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc-and-methanol'
44: 1 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.117 0.059 198.9
44: (ns/day) (hour/ns)
44: Performance: 2.947 8.143
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (83 ms)
44: [----------] 3 tests from Checking/InitialConstraintsTest (243 ms total)
44:
44: [----------] Global test environment tear-down
44: [==========] 51 tests from 9 test cases ran. (15058 ms total)
44: [ PASSED ] 51 tests.
44/54 Test #44: MdrunIOTests ........................ Passed 15.10 sec
test 45
Start 45: MdrunTests
45: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunTests.xml"
45: Test timeout computed to be: 600
45: [==========] Running 24 tests from 7 test cases.
45: [----------] Global test environment set-up.
45: [----------] 1 test from DispersionCorrectionTest
45: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]:
45: The Berendsen thermostat does not generate the correct kinetic energy
45: distribution. You might want to consider using the V-rescale thermostat.
45:
45: Setting the LD random seed to 828130928
45: Generated 2145 of the 2145 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 2145 of the 2145 1-4 parameter combinations
45: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
45: Cleaning up constraints and constant bonded interactions with virtual sites
45: Converted 3 Bonds with virtual sites to connections, 7 left
45: Removed 18 Angles with virtual sites, 21 left
45: Removed 10 Proper Dih.s with virtual sites, 44 left
45: Converted 12 Constraints with virtual sites to connections, 0 left
45: Number of degrees of freedom in T-Coupling group System is 30.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]:
45: There are 9 non-linear virtual site constructions. Their contribution to
45: the energy error is approximated. In most cases this does not affect the
45: error significantly.
45:
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Changing nstlist from 10 to 50, rlist from 1.016 to 1.167
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Alanine dipeptide in vacuo'
45: 200 steps, 0.4 ps.
45: turning H bonds into constraints...
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
45: Calculated rlist for 1x1 atom pair-list as 1.028 nm, buffer size 0.028 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.016 nm, buffer size 0.016 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.319 0.160 199.5
45: (ns/day) (hour/ns)
45: Performance: 217.020 0.111
45: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (250 ms)
45: [----------] 1 test from DispersionCorrectionTest (250 ms total)
45:
45: [----------] 1 test from OriresTest
45: [ RUN ] OriresTest.OriresCanRun
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
45: The Berendsen thermostat does not generate the correct kinetic energy
45: distribution. You might want to consider using the V-rescale thermostat.
45:
45: Setting the LD random seed to 1113394770
45: Generated 2145 of the 2145 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 2145 of the 2145 1-4 parameter combinations
45: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 518.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank.
45: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164
45:
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1'
45: 10 steps, 0.0 ps.
45: turning H bonds into constraints...
45: turning H bonds into constraints...
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
45: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.245 0.123 199.3
45: (ns/day) (hour/ns)
45: Performance: 15.439 1.554
45: [ OK ] OriresTest.OriresCanRun (817 ms)
45: [----------] 1 test from OriresTest (818 ms total)
45:
45: [----------] 3 tests from PmeTest
45: [ RUN ] PmeTest.ReproducesEnergies
45: Setting the LD random seed to -1124438910
45: Generated 8 of the 10 non-bonded parameter combinations
45: Excluding 2 bonded neighbours molecule type 'Methanol'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group rest is 12.00
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
45: NVE simulation: will use the initial temperature of 1046.791 K for
45: determining the Verlet buffer size
45:
45: Estimate for the relative computational load of the PME mesh part: 1.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
45: The optimal PME mesh load for parallel simulations is below 0.5
45: and for highly parallel simulations between 0.25 and 0.33,
45: for higher performance, increase the cut-off and the PME grid spacing.
45:
45:
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 20 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: Calculating fourier grid dimensions for X Y Z
45: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.243 0.122 199.5
45: (ns/day) (hour/ns)
45: Performance: 14.914 1.609
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 20 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.250 0.125 199.5
45: (ns/day) (hour/ns)
45: Performance: 14.478 1.658
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45:
45: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
45: starting mdrun 'spc-and-methanol'
45: 20 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.232 0.116 199.5
45: (ns/day) (hour/ns)
45: Performance: 15.585 1.540
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (464 ms)
45: [ RUN ] PmeTest.ScalesTheBox
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 478141484
45: Generated 8 of the 10 non-bonded parameter combinations
45: Excluding 2 bonded neighbours molecule type 'Methanol'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group rest is 12.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
45: NVE simulation: will use the initial temperature of 1046.791 K for
45: determining the Verlet buffer size
45:
45: Estimate for the relative computational load of the PME mesh part: 1.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
45: The optimal PME mesh load for parallel simulations is below 0.5
45: and for highly parallel simulations between 0.25 and 0.33,
45: for higher performance, increase the cut-off and the PME grid spacing.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 0 steps, 0.0 ps.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.005 0.003 179.7
45: (ns/day) (hour/ns)
45: Performance: 30.358 0.791
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: Calculating fourier grid dimensions for X Y Z
45: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
45: This run will generate roughly 0 Mb of data
45: [ OK ] PmeTest.ScalesTheBox (38 ms)
45: [ RUN ] PmeTest.ScalesTheBoxWithWalls
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 546322231
45: Generated 8 of the 10 non-bonded parameter combinations
45: Excluding 2 bonded neighbours molecule type 'Methanol'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Searching the wall atom type(s)
45: Number of degrees of freedom in T-Coupling group rest is 13.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
45: NVE simulation: will use the initial temperature of 966.268 K for
45: determining the Verlet buffer size
45:
45: Estimate for the relative computational load of the PME mesh part: 1.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
45: The optimal PME mesh load for parallel simulations is below 0.5
45: and for highly parallel simulations between 0.25 and 0.33,
45: for higher performance, increase the cut-off and the PME grid spacing.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 0 steps, 0.0 ps.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.018 0.009 191.2
45: (ns/day) (hour/ns)
45: Performance: 9.263 2.591
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: Calculating fourier grid dimensions for X Y Z
45: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
45: This run will generate roughly 0 Mb of data
45: [ OK ] PmeTest.ScalesTheBoxWithWalls (74 ms)
45: [----------] 3 tests from PmeTest (576 ms total)
45:
45: [----------] 1 test from CompelTest
45: [ RUN ] CompelTest.SwapCanRun
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
45: The Berendsen thermostat does not generate the correct kinetic energy
45: distribution. You might want to consider using the V-rescale thermostat.
45:
45: Setting the LD random seed to 861997162
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 3 bonded neighbours molecule type 'Protein'
45: Excluding 3 bonded neighbours molecule type 'OCT'
45: Excluding 1 bonded neighbours molecule type 'NA'
45: Excluding 1 bonded neighbours molecule type 'CL'
45: Excluding 3 bonded neighbours molecule type 'Protein'
45: Excluding 3 bonded neighbours molecule type 'OCT'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Split0 group 'Ch0' contains 83 atoms.
45: Split1 group 'Ch1' contains 83 atoms.
45: Solvent group 'SOL' contains 11931 atoms.
45: Swap group 'NA+' contains 19 atoms.
45: Swap group 'CL-' contains 19 atoms.
45: Number of degrees of freedom in T-Coupling group System is 27869.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
45: Removing center of mass motion in the presence of position restraints
45: might cause artifacts. When you are using position restraints to
45: equilibrate a macro-molecule, the artifacts are usually negligible.
45:
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: SWAP: Determining initial numbers of ions per compartment.
45: SWAP: Setting pointers for checkpoint writing
45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
45: starting mdrun 'Channel_coco in octane membrane'
45: 2 steps, 0.0 ps.
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
45: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 1 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 2.869 1.435 199.9
45: (ns/day) (hour/ns)
45: Performance: 0.903 26.576
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: SWAP: Setting pointers for checkpoint writing
45: SWAP: Copying channel fluxes from checkpoint file data
45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
45: starting mdrun 'Channel_coco in octane membrane'
45: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 2.611 1.306 199.9
45: (ns/day) (hour/ns)
45: Performance: 0.992 24.184
45: [ OK ] CompelTest.SwapCanRun (6296 ms)
45: [----------] 1 test from CompelTest (6296 ms total)
45:
45: [----------] 6 tests from BondedInteractionsTest
45: [ RUN ] BondedInteractionsTest.NormalBondWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 1904112400
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 2 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.002 0.001 178.4
45: (ns/day) (hour/ns)
45: Performance: 92.117 0.261
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.NormalBondWorks (23 ms)
45: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -1707321892
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 2 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.001 0.001 176.9
45: (ns/day) (hour/ns)
45: Performance: 103.303 0.232
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.TabulatedBondWorks (27 ms)
45: [ RUN ] BondedInteractionsTest.NormalAngleWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 1602752624
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.001 0.001 177.3
45: (ns/day) (hour/ns)
45: Performance: 103.244 0.232
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.NormalAngleWorks (21 ms)
45: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 1988202144
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.001 0.001 176.2
45: (ns/day) (hour/ns)
45: Performance: 104.344 0.230
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (24 ms)
45: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 1631256596
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.001 0.001 177.1
45: (ns/day) (hour/ns)
45: Performance: 105.254 0.228
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.NormalDihedralWorks (21 ms)
45: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 488258556
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.001 0.001 175.7
45: (ns/day) (hour/ns)
45: Performance: 106.054 0.226
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (27 ms)
45: [----------] 6 tests from BondedInteractionsTest (144 ms total)
45:
45: [----------] 4 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest
45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 1 of the 1 non-bonded parameter combinations
45: Excluding 1 bonded neighbours molecule type 'Argon'
45: Number of degrees of freedom in T-Coupling group System is 33.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
45: NVE simulation: will use the initial temperature of 68.810 K for
45: determining the Verlet buffer size
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.169 0.085 199.5
45: (ns/day) (hour/ns)
45: Performance: 17.307 1.387
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.151 0.076 199.3
45: (ns/day) (hour/ns)
45: Performance: 19.402 1.237
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016 trr version: GMX_trn_file (double precision)
45:
45:
45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 (202 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 1 of the 1 non-bonded parameter combinations
45: Excluding 1 bonded neighbours molecule type 'Argon'
45: Number of degrees of freedom in T-Coupling group System is 33.00
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.198 0.099 199.6
45: (ns/day) (hour/ns)
45: Performance: 14.772 1.625
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.184 0.092 199.4
45: (ns/day) (hour/ns)
45: Performance: 15.903 1.509
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 (234 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 27.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
45: NVE simulation: will use the initial temperature of 398.997 K for
45: determining the Verlet buffer size
45:
45:
45: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 4 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
45: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.208 0.104 199.6
45: (ns/day) (hour/ns)
45: Performance: 14.110 1.701
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.179 0.090 199.3
45: (ns/day) (hour/ns)
45: Performance: 16.397 1.464
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 (2743 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 27.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
45: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.241 0.121 199.6
45: (ns/day) (hour/ns)
45: Performance: 12.179 1.971
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.194 0.098 199.4
45: (ns/day) (hour/ns)
45: Performance: 15.057 1.594
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 (2766 ms)
45: [----------] 4 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest (5946 ms total)
45:
45: [----------] 8 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 1 of the 1 non-bonded parameter combinations
45: Excluding 1 bonded neighbours molecule type 'Argon'
45: Number of degrees of freedom in T-Coupling group System is 33.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
45: NVE simulation: will use the initial temperature of 68.810 K for
45: determining the Verlet buffer size
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.173 0.087 199.4
45: (ns/day) (hour/ns)
45: Performance: 16.881 1.422
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.170 0.085 199.6
45: (ns/day) (hour/ns)
45: Performance: 17.231 1.393
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 (214 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 1 of the 1 non-bonded parameter combinations
45: Excluding 1 bonded neighbours molecule type 'Argon'
45: Number of degrees of freedom in T-Coupling group System is 33.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
45: NVE simulation: will use the initial temperature of 68.810 K for
45: determining the Verlet buffer size
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.213 0.107 199.4
45: (ns/day) (hour/ns)
45: Performance: 13.765 1.744
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.220 0.110 199.6
45: (ns/day) (hour/ns)
45: Performance: 13.318 1.802
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 (260 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 1 of the 1 non-bonded parameter combinations
45: Excluding 1 bonded neighbours molecule type 'Argon'
45: Number of degrees of freedom in T-Coupling group System is 33.00
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.193 0.097 199.4
45: (ns/day) (hour/ns)
45: Performance: 15.158 1.583
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.187 0.093 199.6
45: (ns/day) (hour/ns)
45: Performance: 15.713 1.527
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 (232 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 1 of the 1 non-bonded parameter combinations
45: Excluding 1 bonded neighbours molecule type 'Argon'
45: Number of degrees of freedom in T-Coupling group System is 33.00
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.229 0.115 199.4
45: (ns/day) (hour/ns)
45: Performance: 12.794 1.876
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.220 0.110 199.6
45: (ns/day) (hour/ns)
45: Performance: 13.342 1.799
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 (268 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 27.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
45: NVE simulation: will use the initial temperature of 398.997 K for
45: determining the Verlet buffer size
45:
45:
45: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 4 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
45: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.263 0.132 199.5
45: (ns/day) (hour/ns)
45: Performance: 11.134 2.156
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.214 0.107 199.6
45: (ns/day) (hour/ns)
45: Performance: 13.671 1.756
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 (2792 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 27.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
45: NVE simulation: will use the initial temperature of 398.997 K for
45: determining the Verlet buffer size
45:
45:
45: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 4 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
45: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.230 0.116 199.4
45: (ns/day) (hour/ns)
45: Performance: 12.712 1.888
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.198 0.099 199.6
45: (ns/day) (hour/ns)
45: Performance: 14.829 1.618
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 (2776 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 27.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
45: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.283 0.142 199.6
45: (ns/day) (hour/ns)
45: Performance: 10.350 2.319
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.325 0.163 199.7
45: (ns/day) (hour/ns)
45: Performance: 9.017 2.662
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 (2857 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 27.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
45: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.289 0.145 199.5
45: (ns/day) (hour/ns)
45: Performance: 10.125 2.370
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
45: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.297 0.149 199.7
45: (ns/day) (hour/ns)
45: Performance: 9.874 2.431
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 (2850 ms)
45: [----------] 8 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (12250 ms total)
45:
45: [----------] Global test environment tear-down
45: [==========] 24 tests from 7 test cases ran. (26281 ms total)
45: [ PASSED ] 24 tests.
45/54 Test #45: MdrunTests .......................... Passed 26.31 sec
test 46
Start 46: MdrunNonIntegratorTests
46: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml"
46: Test timeout computed to be: 600
46: [==========] Running 65 tests from 7 test cases.
46: [----------] Global test environment set-up.
46: [----------] 1 test from NonbondedBenchTest
46: [ RUN ] NonbondedBenchTest.BasicEndToEndTest
46: System size: 3000 atoms
46: Cut-off radius: 1 nm
46: Number of threads: 1
46: Number of iterations: 1
46: Compute energies: no
46: Ewald excl. corr.: analytical
46:
46: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle
46: total useful
46: Ewald all geom. no 0.000 0.0000 inf inf
46: [ OK ] NonbondedBenchTest.BasicEndToEndTest (254 ms)
46: [----------] 1 test from NonbondedBenchTest (254 ms total)
46:
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -4.79910463671071e+01
46: Maximum force = 1.86297359432220e+02 on atom 13
46: Norm of force = 8.77219865482161e+01
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (1099 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 3.02331e+02 on atom 3
46: F-Norm = 1.18024e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -5.58622538633290e+01
46: Maximum force = 4.27274822366523e+02 on atom 13
46: Norm of force = 1.84530029253828e+02
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (2518 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.19376899751521e+02
46: Maximum force = 9.99884921009767e+03 on atom 9
46: Norm of force = 4.61669565054298e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (445 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46:
46: NOTE 3 [file glycine_vacuo.top, line 12]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41575e+04 on atom 10
46: F-Norm = 1.18451e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.51743018140925e+02
46: Maximum force = 7.42089573409111e+03 on atom 9
46: Norm of force = 3.56929298615739e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (446 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.56984193848276e+02
46: Maximum force = 4.56923624626296e+02 on atom 17
46: Norm of force = 1.83258377168331e+02
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (73 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46:
46: NOTE 4 [file unknown]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 1.06800e+03 on atom 28
46: F-Norm = 4.26922e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.69410778678185e+02
46: Maximum force = 2.18225948473957e+02 on atom 17
46: Norm of force = 7.92068036537697e+01
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (75 ms)
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (4656 ms total)
46:
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents converged to Fmax < 10 in 1 steps
46: Potential Energy = -9.74257075835450e-01
46: Maximum force = 4.01322929015108e+00 on atom 1
46: Norm of force = 1.63839399694368e+00
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (24 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 4.01323e+00 on atom 1
46: F-Norm = 1.63839e+00
46:
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
46: Potential Energy = -9.90642313893957e-01
46: Maximum force = 2.57812909491105e+00 on atom 1
46: Norm of force = 1.05251679559258e+00
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (24 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46:
46: There was 1 warning
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Low-Memory BFGS Minimizer:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: Using 10 BFGS correction steps.
46:
46: F-max = 4.01323e+00 on atom 1
46: F-Norm = 1.63839e+00
46:
46:
46: writing lowest energy coordinates.
46:
46: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
46: Potential Energy = -9.90642313893957e-01
46: Maximum force = 2.57812909491105e+00 on atom 1
46: Norm of force = 1.05251679559258e+00
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (24 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.19395484891517e+02
46: Maximum force = 9.97041707197910e+03 on atom 9
46: Norm of force = 4.62274878665467e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (449 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41672e+04 on atom 10
46: F-Norm = 1.19357e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.56258793899479e+02
46: Maximum force = 7.50181017480397e+03 on atom 9
46: Norm of force = 3.61390332564874e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (454 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46:
46: There was 1 warning
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Low-Memory BFGS Minimizer:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: Using 10 BFGS correction steps.
46:
46: F-max = 2.41672e+04 on atom 10
46: F-Norm = 1.19357e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 5.61116097794203e+02
46: Maximum force = 1.26854826291223e+04 on atom 10
46: Norm of force = 6.06436286976271e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (453 ms)
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1428 ms total)
46:
46: [----------] 5 tests from NormalModesWorks/NormalModesTest
46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 3 of the 3 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 3 of the 3 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 15.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Small system size (N=6), using full Hessian format.
46: Allocating Hessian memory...
46:
46: starting normal mode calculation '2 scaled waters'
46: 12 steps.
46:
46: Maximum force: 9.96989e-06
46:
46:
46: Writing Hessian...
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Reading double precision matrix generated by GROMACS 2020.4-Raspbian-2020.4-2
46:
46: Diagonalizing to find vectors 7 through 18...
46: Writing eigenvalues...
46:
46: Writing average structure & eigenvectors 7--18 to eigenvec.trr
46: This run will generate roughly 0 Mb of data
46: There are: 6 Atoms
46: Using begin = 7 and end = 18
46: Full matrix storage format, nrow=18, ncols=18
46: Writing eigenfrequencies - negative eigenvalues will be set to zero.
46: Cannot compute entropy when -first = 7
46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (32 ms)
46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
46:
46: NOTE 3 [file villin.top, line 2452]:
46: System has non-zero total charge: -2.000000
46: Total charge should normally be an integer. See
46: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
46: for discussion on how close it should be to an integer.
46:
46:
46:
46: Number of degrees of freedom in T-Coupling group System is 765.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Small system size (N=256), using full Hessian format.
46: Allocating Hessian memory...
46:
46: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN'
46: 512 steps.
46:
46: Maximum force: 6.97568e-04
46:
46:
46: Writing Hessian...
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Reading double precision matrix generated by GROMACS 2020.4-Raspbian-2020.4-2
46:
46: Diagonalizing to find vectors 7 through 50...
46: Writing eigenvalues...
46:
46: Writing average structure & eigenvectors 7--50 to eigenvec.trr
46: This run will generate roughly 0 Mb of data
46: There are: 256 Atoms
46: Using begin = 7 and end = 50
46: Full matrix storage format, nrow=768, ncols=768
46: Writing eigenfrequencies - negative eigenvalues will be set to zero.
46: Cannot compute entropy when -first = 7
46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (9890 ms)
46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 15.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Small system size (N=6), using full Hessian format.
46: Allocating Hessian memory...
46:
46: starting normal mode calculation 'flex spc dimer'
46: 12 steps.
46:
46: Maximum force: 3.36401e-04
46:
46:
46: Writing Hessian...
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Reading double precision matrix generated by GROMACS 2020.4-Raspbian-2020.4-2
46:
46: Diagonalizing to find vectors 7 through 18...
46: Writing eigenvalues...
46:
46: Writing average structure & eigenvectors 7--18 to eigenvec.trr
46: This run will generate roughly 0 Mb of data
46: There are: 6 Atoms
46: Using begin = 7 and end = 18
46: Full matrix storage format, nrow=18, ncols=18
46: Writing eigenfrequencies - negative eigenvalues will be set to zero.
46: Cannot compute entropy when -first = 7
46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (2532 ms)
46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Number of degrees of freedom in T-Coupling group System is 6.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Small system size (N=3), using full Hessian format.
46: Allocating Hessian memory...
46:
46: starting normal mode calculation '1 TIP5P'
46: 6 steps.
46:
46: Maximum force: 2.42882e-04
46:
46:
46: Writing Hessian...
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Reading double precision matrix generated by GROMACS 2020.4-Raspbian-2020.4-2
46:
46: Diagonalizing to find vectors 7 through 9...
46: Writing eigenvalues...
46:
46: Writing average structure & eigenvectors 7--9 to eigenvec.trr
46: This run will generate roughly 0 Mb of data
46: There are: 3 Atoms
46: There are: 2 VSites
46: Using begin = 7 and end = 9
46: Full matrix storage format, nrow=9, ncols=9
46: Writing eigenfrequencies - negative eigenvalues will be set to zero.
46: Cannot compute entropy when -first = 7
46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (2515 ms)
46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46: Generated 6 of the 10 non-bonded parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SW'
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Number of degrees of freedom in T-Coupling group System is 15.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Small system size (N=6), using full Hessian format.
46: Allocating Hessian memory...
46:
46: starting normal mode calculation 'sw dimer'
46: 12 steps.
46:
46: Maximum force: 1.07599e-03
46: The force is probably not small enough to ensure that you are at a minimum.
46: Be aware that negative eigenvalues may occur
46: when the resulting matrix is diagonalized.
46:
46:
46: Writing Hessian...
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Reading double precision matrix generated by GROMACS 2020.4-Raspbian-2020.4-2
46:
46: Diagonalizing to find vectors 7 through 18...
46: Writing eigenvalues...
46:
46: Writing average structure & eigenvectors 7--18 to eigenvec.trr
46: This run will generate roughly 0 Mb of data
46: There are: 6 Atoms
46: There are: 2 Shells
46: There are: 2 VSites
46:
46: NOTE: in the current version shell prediction during the crun is disabled
46:
46: Using begin = 7 and end = 18
46: Full matrix storage format, nrow=18, ncols=18
46: Writing eigenfrequencies - negative eigenvalues will be set to zero.
46: Cannot compute entropy when -first = 7
46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (33 ms)
46: [----------] 5 tests from NormalModesWorks/NormalModesTest (15004 ms total)
46:
46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
46: NVE simulation: will use the initial temperature of 68.810 K for
46: determining the Verlet buffer size
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.196 0.098 199.5
46: (ns/day) (hour/ns)
46: Performance: 14.960 1.604
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr'
46:
46: trr version: GMX_trn_file (double precision)
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.012 0.006 196.3
46: (ns/day) (hour/ns)
46: Performance: 239.572 0.100
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (143 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
46: NVE simulation: will use the initial temperature of 68.810 K for
46: determining the Verlet buffer size
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.194 0.097 199.6
46: (ns/day) (hour/ns)
46: Performance: 15.139 1.585
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.012 0.006 196.3
46: (ns/day) (hour/ns)
46: Performance: 239.377 0.100
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (142 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
46: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.209 0.105 199.5
46: (ns/day) (hour/ns)
46: Performance: 14.037 1.710
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.012 0.006 196.2
46: (ns/day) (hour/ns)
46: Performance: 240.001 0.100
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (150 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.242 0.121 199.6
46: (ns/day) (hour/ns)
46: Performance: 12.117 1.981
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.012 0.006 196.3
46: (ns/day) (hour/ns)
46: Performance: 238.810 0.100
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (167 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: NVE simulation: will use the initial temperature of 398.997 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.282 0.141 199.6
46: (ns/day) (hour/ns)
46: Performance: 10.380 2.312
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 196.4
46: (ns/day) (hour/ns)
46: Performance: 209.387 0.115
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (2680 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: NVE simulation: will use the initial temperature of 398.997 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.263 0.132 199.7
46: (ns/day) (hour/ns)
46: Performance: 11.161 2.150
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 196.3
46: (ns/day) (hour/ns)
46: Performance: 205.827 0.117
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (2667 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.271 0.136 199.6
46: (ns/day) (hour/ns)
46: Performance: 10.813 2.220
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 196.4
46: (ns/day) (hour/ns)
46: Performance: 201.709 0.119
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (2675 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.204 0.102 199.4
46: (ns/day) (hour/ns)
46: Performance: 14.351 1.672
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 196.4
46: (ns/day) (hour/ns)
46: Performance: 205.758 0.117
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (2641 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: NVE simulation: will use the initial temperature of 456.887 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 6 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.267 0.134 199.4
46: (ns/day) (hour/ns)
46: Performance: 10.969 2.188
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.024 0.012 197.1
46: (ns/day) (hour/ns)
46: Performance: 120.555 0.199
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (246 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: NVE simulation: will use the initial temperature of 456.887 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 6 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.259 0.130 199.4
46: (ns/day) (hour/ns)
46: Performance: 11.312 2.122
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.024 0.012 197.0
46: (ns/day) (hour/ns)
46: Performance: 120.678 0.199
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (241 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.275 0.138 199.4
46: (ns/day) (hour/ns)
46: Performance: 10.651 2.253
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.024 0.012 196.8
46: (ns/day) (hour/ns)
46: Performance: 119.868 0.200
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (301 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.241 0.121 199.3
46: (ns/day) (hour/ns)
46: Performance: 12.161 1.974
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.024 0.012 197.0
46: (ns/day) (hour/ns)
46: Performance: 119.340 0.201
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (267 ms)
46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (12320 ms total)
46:
46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.323 0.162 199.4
46: (ns/day) (hour/ns)
46: Performance: 9.062 2.648
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.0
46: (ns/day) (hour/ns)
46: Performance: 95.979 0.250
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (283 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.240 0.121 199.1
46: (ns/day) (hour/ns)
46: Performance: 12.182 1.970
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.0
46: (ns/day) (hour/ns)
46: Performance: 96.425 0.249
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (241 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.207 0.104 199.1
46: (ns/day) (hour/ns)
46: Performance: 14.131 1.698
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.8
46: (ns/day) (hour/ns)
46: Performance: 96.012 0.250
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (224 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.272 0.137 199.3
46: (ns/day) (hour/ns)
46: Performance: 10.744 2.234
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.0
46: (ns/day) (hour/ns)
46: Performance: 96.282 0.249
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (258 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.290 0.145 199.3
46: (ns/day) (hour/ns)
46: Performance: 10.102 2.376
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.0
46: (ns/day) (hour/ns)
46: Performance: 96.256 0.249
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (266 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.257 0.129 199.3
46: (ns/day) (hour/ns)
46: Performance: 11.397 2.106
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.8
46: (ns/day) (hour/ns)
46: Performance: 96.253 0.249
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (250 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.207 0.104 199.1
46: (ns/day) (hour/ns)
46: Performance: 14.131 1.698
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.1
46: (ns/day) (hour/ns)
46: Performance: 96.619 0.248
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (225 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.258 0.129 199.3
46: (ns/day) (hour/ns)
46: Performance: 11.356 2.113
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.2
46: (ns/day) (hour/ns)
46: Performance: 95.390 0.252
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (250 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.357 0.179 199.5
46: (ns/day) (hour/ns)
46: Performance: 8.205 2.925
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.1
46: (ns/day) (hour/ns)
46: Performance: 96.628 0.248
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (300 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.257 0.129 199.2
46: (ns/day) (hour/ns)
46: Performance: 11.365 2.112
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.1
46: (ns/day) (hour/ns)
46: Performance: 96.297 0.249
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (250 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.224 0.113 199.1
46: (ns/day) (hour/ns)
46: Performance: 13.040 1.841
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.7
46: (ns/day) (hour/ns)
46: Performance: 96.261 0.249
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (233 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.243 0.122 199.5
46: (ns/day) (hour/ns)
46: Performance: 12.064 1.989
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.0
46: (ns/day) (hour/ns)
46: Performance: 96.205 0.249
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (242 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.342 0.171 199.6
46: (ns/day) (hour/ns)
46: Performance: 8.570 2.800
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.0
46: (ns/day) (hour/ns)
46: Performance: 96.517 0.249
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (292 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.293 0.147 199.6
46: (ns/day) (hour/ns)
46: Performance: 10.014 2.397
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.2
46: (ns/day) (hour/ns)
46: Performance: 96.443 0.249
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (267 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.292 0.146 199.6
46: (ns/day) (hour/ns)
46: Performance: 10.034 2.392
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.1
46: (ns/day) (hour/ns)
46: Performance: 96.617 0.248
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (266 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.375 0.188 199.7
46: (ns/day) (hour/ns)
46: Performance: 7.818 3.070
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.6
46: (ns/day) (hour/ns)
46: Performance: 95.900 0.250
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (309 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.275 0.138 199.6
46: (ns/day) (hour/ns)
46: Performance: 10.646 2.254
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.1
46: (ns/day) (hour/ns)
46: Performance: 96.702 0.248
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (258 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.310 0.155 199.6
46: (ns/day) (hour/ns)
46: Performance: 9.471 2.534
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.1
46: (ns/day) (hour/ns)
46: Performance: 96.387 0.249
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (275 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.242 0.121 199.5
46: (ns/day) (hour/ns)
46: Performance: 12.095 1.984
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.8
46: (ns/day) (hour/ns)
46: Performance: 96.028 0.250
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (242 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.309 0.155 199.6
46: (ns/day) (hour/ns)
46: Performance: 9.494 2.528
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.1
46: (ns/day) (hour/ns)
46: Performance: 95.992 0.250
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (274 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.292 0.146 199.6
46: (ns/day) (hour/ns)
46: Performance: 10.045 2.389
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.5
46: (ns/day) (hour/ns)
46: Performance: 95.874 0.250
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (266 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.225 0.113 199.5
46: (ns/day) (hour/ns)
46: Performance: 13.012 1.844
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.1
46: (ns/day) (hour/ns)
46: Performance: 96.312 0.249
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (233 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.319 0.160 199.4
46: (ns/day) (hour/ns)
46: Performance: 9.182 2.614
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.1
46: (ns/day) (hour/ns)
46: Performance: 96.184 0.250
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (318 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.232 0.117 199.2
46: (ns/day) (hour/ns)
46: Performance: 12.598 1.905
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.8
46: (ns/day) (hour/ns)
46: Performance: 96.222 0.249
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (276 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.249 0.125 199.2
46: (ns/day) (hour/ns)
46: Performance: 11.767 2.040
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.1
46: (ns/day) (hour/ns)
46: Performance: 96.196 0.249
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (283 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.249 0.125 199.2
46: (ns/day) (hour/ns)
46: Performance: 11.753 2.042
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.4
46: (ns/day) (hour/ns)
46: Performance: 95.141 0.252
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (283 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.264 0.133 199.3
46: (ns/day) (hour/ns)
46: Performance: 11.067 2.169
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.1
46: (ns/day) (hour/ns)
46: Performance: 96.241 0.249
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (290 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.249 0.125 199.2
46: (ns/day) (hour/ns)
46: Performance: 11.744 2.044
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.1
46: (ns/day) (hour/ns)
46: Performance: 96.265 0.249
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (283 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.266 0.133 199.3
46: (ns/day) (hour/ns)
46: Performance: 11.006 2.181
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.9
46: (ns/day) (hour/ns)
46: Performance: 96.135 0.250
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (291 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.282 0.142 199.3
46: (ns/day) (hour/ns)
46: Performance: 10.365 2.315
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.9
46: (ns/day) (hour/ns)
46: Performance: 96.193 0.249
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (299 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.266 0.134 199.3
46: (ns/day) (hour/ns)
46: Performance: 11.001 2.182
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.6
46: (ns/day) (hour/ns)
46: Performance: 95.241 0.252
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (293 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.265 0.133 199.3
46: (ns/day) (hour/ns)
46: Performance: 11.061 2.170
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 195.9
46: (ns/day) (hour/ns)
46: Performance: 95.550 0.251
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (291 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.765 0.383 199.7
46: (ns/day) (hour/ns)
46: Performance: 3.836 6.257
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.030 0.015 196.0
46: (ns/day) (hour/ns)
46: Performance: 95.253 0.252
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (541 ms)
46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (9159 ms total)
46:
46: [----------] 2 tests from Angles1/SimpleMdrunTest
46: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46: Generated 3 of the 3 non-bonded parameter combinations
46: Excluding 3 bonded neighbours molecule type 'butane'
46:
46: NOTE 2 [file angles1.top, line 72]:
46: In moleculetype 'butane' 4 atoms are not bound by a potential or
46: constraint to any other atom in the same moleculetype. Although
46: technically this might not cause issues in a simulation, this often means
46: that the user forgot to add a bond/potential/constraint or put multiple
46: molecules in the same moleculetype definition by mistake. Run with -v to
46: get information for each atom.
46:
46: Number of degrees of freedom in T-Coupling group System is 9.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]:
46: NVE simulation: will use the initial temperature of 238.919 K for
46: determining the Verlet buffer size
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'This_incredible_box_of_butane'
46: 50 steps, 0.1 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K
46: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.263 0.132 199.6
46: (ns/day) (hour/ns)
46: Performance: 33.497 0.716
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 5 time 0.020
Reading energy frame 6 time 0.024
Reading energy frame 7 time 0.028
Reading energy frame 8 time 0.032
Reading energy frame 9 time 0.036
Reading energy frame 10 time 0.040
Reading energy frame 11 time 0.044
Reading energy frame 12 time 0.048
Reading energy frame 13 time 0.050
Last energy frame read 13 time 0.050
46: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (164 ms)
46: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46: Generated 3 of the 3 non-bonded parameter combinations
46: Excluding 3 bonded neighbours molecule type 'butane'
46:
46: NOTE 2 [file angles1.top, line 72]:
46: In moleculetype 'butane' 4 atoms are not bound by a potential or
46: constraint to any other atom in the same moleculetype. Although
46: technically this might not cause issues in a simulation, this often means
46: that the user forgot to add a bond/potential/constraint or put multiple
46: molecules in the same moleculetype definition by mistake. Run with -v to
46: get information for each atom.
46:
46: Number of degrees of freedom in T-Coupling group System is 9.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]:
46: NVE simulation: will use the initial temperature of 238.919 K for
46: determining the Verlet buffer size
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'This_incredible_box_of_butane'
46: 50 steps, 0.1 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K
46: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.318 0.159 199.8
46: (ns/day) (hour/ns)
46: Performance: 27.682 0.867
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 5 time 0.020
Reading energy frame 6 time 0.024
Reading energy frame 7 time 0.028
Reading energy frame 8 time 0.032
Reading energy frame 9 time 0.036
Reading energy frame 10 time 0.040
Reading energy frame 11 time 0.044
Reading energy frame 12 time 0.048
Reading energy frame 13 time 0.050
Last energy frame read 13 time 0.050
46: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (191 ms)
46: [----------] 2 tests from Angles1/SimpleMdrunTest (356 ms total)
46:
46: [----------] Global test environment tear-down
46: [==========] 65 tests from 7 test cases ran. (43177 ms total)
46: [ PASSED ] 65 tests.
46/54 Test #46: MdrunNonIntegratorTests ............. Passed 43.25 sec
test 47
Start 47: MdrunTpiTests
47: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml"
47: Test timeout computed to be: 600
47: [==========] Running 2 tests from 1 test case.
47: [----------] Global test environment set-up.
47: [----------] 2 tests from Simple/TpiTest
47: [ RUN ] Simple/TpiTest.ReproducesOutput/0
47: Ignoring obsolete mdp entry 'ns_type'
47: Generated 331705 of the 331705 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 331705 of the 331705 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Excluding 3 bonded neighbours molecule type 'methane'
47: Number of degrees of freedom in T-Coupling group System is 1308.00
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
47: TPI is not implemented for GPUs.
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: Reading frames from gro file '216 water molecules', 648 atoms.
47:
Reading frame 0 time 0.000 mu 8.706e+02 <mu> 8.706e+02
47:
Last frame 0 time 0.000
47: Analysing residue names:
47: There are: 216 Water residues
47: There are: 1 Other residues
47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
47: This run will generate roughly 0 Mb of data
47: [ OK ] Simple/TpiTest.ReproducesOutput/0 (1266 ms)
47: [ RUN ] Simple/TpiTest.ReproducesOutput/1
47: Ignoring obsolete mdp entry 'ns_type'
47: Generated 331705 of the 331705 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 331705 of the 331705 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Excluding 3 bonded neighbours molecule type 'methane'
47: Number of degrees of freedom in T-Coupling group System is 1308.00
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
47: TPI is not implemented for GPUs.
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: Reading frames from gro file '216 water molecules', 648 atoms.
47:
Reading frame 0 time 0.000 mu 9.144e+01 <mu> 9.144e+01
47:
Last frame 0 time 0.000
47: Analysing residue names:
47: There are: 216 Water residues
47: There are: 1 Other residues
47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
47: This run will generate roughly 0 Mb of data
47: [ OK ] Simple/TpiTest.ReproducesOutput/1 (2702 ms)
47: [----------] 2 tests from Simple/TpiTest (3968 ms total)
47:
47: [----------] Global test environment tear-down
47: [==========] 2 tests from 1 test case ran. (3968 ms total)
47: [ PASSED ] 2 tests.
47/54 Test #47: MdrunTpiTests ....................... Passed 3.99 sec
test 48
Start 48: MdrunMpiTests
48: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml"
48: Test timeout computed to be: 600
48: [==========] Running 22 tests from 7 test cases.
48: [----------] Global test environment set-up.
48: [----------] 1 test from DomainDecompositionSpecialCasesTest
48: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -1549293112
48: Generated 3 of the 3 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 3 of the 3 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 9.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 0 steps, 0.0 ps.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.003 0.001 244.5
48: (ns/day) (hour/ns)
48: Performance: 69.376 0.346
48: This run will generate roughly 0 Mb of data
48: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (46 ms)
48: [----------] 1 test from DomainDecompositionSpecialCasesTest (46 ms total)
48:
48: [----------] 4 tests from MimicTest
48: [ RUN ] MimicTest.OneQuantumMol
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to 50546507
48: Generated 10 of the 10 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 10 of the 10 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 21.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
48:
48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.005 0.001 355.7
48: (ns/day) (hour/ns)
48: Performance: 57.968 0.414
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.OneQuantumMol (27 ms)
48: [ RUN ] MimicTest.AllQuantumMol
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to 897697551
48: Generated 10 of the 10 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 10 of the 10 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 21.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
48:
48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.005 0.002 360.9
48: (ns/day) (hour/ns)
48: Performance: 57.467 0.418
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.AllQuantumMol (26 ms)
48: [ RUN ] MimicTest.TwoQuantumMol
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -1604503670
48: Generated 10 of the 10 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 10 of the 10 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 21.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
48:
48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.005 0.001 358.5
48: (ns/day) (hour/ns)
48: Performance: 57.797 0.415
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.TwoQuantumMol (26 ms)
48: [ RUN ] MimicTest.BondCuts
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to 1332014404
48: Generated 2211 of the 2211 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 2211 of the 2211 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
48: Number of degrees of freedom in T-Coupling group rest is 66.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
48: NVE simulation: will use the initial temperature of 300.368 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
48:
48: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.007 0.002 369.2
48: (ns/day) (hour/ns)
48: Performance: 43.395 0.553
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
48: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.BondCuts (77 ms)
48: [----------] 4 tests from MimicTest (156 ms total)
48:
48: [----------] 1 test from MultiSimTerminationTest
48: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
48: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
48: [----------] 1 test from MultiSimTerminationTest (0 ms total)
48:
48: [----------] 3 tests from PmeTest
48: [ RUN ] PmeTest.ReproducesEnergies
48: Setting the LD random seed to -606780551
48: Generated 8 of the 10 non-bonded parameter combinations
48: Excluding 2 bonded neighbours molecule type 'Methanol'
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 12.00
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
48: NVE simulation: will use the initial temperature of 1046.791 K for
48: determining the Verlet buffer size
48:
48: Estimate for the relative computational load of the PME mesh part: 1.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
48: The optimal PME mesh load for parallel simulations is below 0.5
48: and for highly parallel simulations between 0.25 and 0.33,
48: for higher performance, increase the cut-off and the PME grid spacing.
48:
48:
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 20 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: Calculating fourier grid dimensions for X Y Z
48: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.605 0.152 399.0
48: (ns/day) (hour/ns)
48: Performance: 11.973 2.005
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 20 steps, 0.0 ps.
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.492 0.123 398.8
48: (ns/day) (hour/ns)
48: Performance: 14.717 1.631
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
48: starting mdrun 'spc-and-methanol'
48: 20 steps, 0.0 ps.
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.527 0.132 398.9
48: (ns/day) (hour/ns)
48: Performance: 13.739 1.747
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (512 ms)
48: [ RUN ] PmeTest.ScalesTheBox
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -1113407221
48: Generated 8 of the 10 non-bonded parameter combinations
48: Excluding 2 bonded neighbours molecule type 'Methanol'
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 12.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
48: NVE simulation: will use the initial temperature of 1046.791 K for
48: determining the Verlet buffer size
48:
48: Estimate for the relative computational load of the PME mesh part: 1.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
48: The optimal PME mesh load for parallel simulations is below 0.5
48: and for highly parallel simulations between 0.25 and 0.33,
48: for higher performance, increase the cut-off and the PME grid spacing.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 0 steps, 0.0 ps.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.010 0.003 350.6
48: (ns/day) (hour/ns)
48: Performance: 29.572 0.812
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: Calculating fourier grid dimensions for X Y Z
48: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
48: This run will generate roughly 0 Mb of data
48: [ OK ] PmeTest.ScalesTheBox (38 ms)
48: [ RUN ] PmeTest.ScalesTheBoxWithWalls
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -959271859
48: Generated 8 of the 10 non-bonded parameter combinations
48: Excluding 2 bonded neighbours molecule type 'Methanol'
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Searching the wall atom type(s)
48: Number of degrees of freedom in T-Coupling group rest is 13.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
48: NVE simulation: will use the initial temperature of 966.268 K for
48: determining the Verlet buffer size
48:
48: Estimate for the relative computational load of the PME mesh part: 1.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
48: The optimal PME mesh load for parallel simulations is below 0.5
48: and for highly parallel simulations between 0.25 and 0.33,
48: for higher performance, increase the cut-off and the PME grid spacing.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 0 steps, 0.0 ps.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.036 0.009 379.6
48: (ns/day) (hour/ns)
48: Performance: 9.217 2.604
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: Calculating fourier grid dimensions for X Y Z
48: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
48: This run will generate roughly 0 Mb of data
48: [ OK ] PmeTest.ScalesTheBoxWithWalls (76 ms)
48: [----------] 3 tests from PmeTest (626 ms total)
48:
48: [----------] 1 test from ReplicaExchangeTerminationTest
48: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
48: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
48: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total)
48:
48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -4.79910463671071e+01
48: Maximum force = 1.86297359432218e+02 on atom 13
48: Norm of force = 8.77219865482161e+01
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (2543 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 3.02331e+02 on atom 3
48: F-Norm = 1.18024e+02
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -5.58622538633290e+01
48: Maximum force = 4.27274822366538e+02 on atom 13
48: Norm of force = 1.84530029253833e+02
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (2541 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 22.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 3.19376899751521e+02
48: Maximum force = 9.99884921009767e+03 on atom 9
48: Norm of force = 4.61669565054298e+03
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (476 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48:
48: NOTE 3 [file glycine_vacuo.top, line 12]:
48: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
48:
48: Number of degrees of freedom in T-Coupling group System is 22.00
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 2.41575e+04 on atom 10
48: F-Norm = 1.18451e+04
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 1.51743018140926e+02
48: Maximum force = 7.42089573409112e+03 on atom 9
48: Norm of force = 3.56929298615739e+03
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (465 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 2145 of the 2145 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 2145 of the 2145 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
48:
48: NOTE 3 [file unknown]:
48: You are using constraints on all bonds, whereas the forcefield has been
48: parametrized only with constraints involving hydrogen atoms. We suggest
48: using constraints = h-bonds instead, this will also improve performance.
48:
48: Cleaning up constraints and constant bonded interactions with virtual sites
48: Removed 18 Angles with virtual sites, 21 left
48: Removed 10 Proper Dih.s with virtual sites, 44 left
48: Converted 15 Constraints with virtual sites to connections, 7 left
48: Number of degrees of freedom in T-Coupling group System is 23.00
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -1.56984193848276e+02
48: Maximum force = 4.56923624626296e+02 on atom 17
48: Norm of force = 1.83258377168331e+02
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (79 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 2145 of the 2145 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 2145 of the 2145 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
48:
48: NOTE 3 [file unknown]:
48: You are using constraints on all bonds, whereas the forcefield has been
48: parametrized only with constraints involving hydrogen atoms. We suggest
48: using constraints = h-bonds instead, this will also improve performance.
48:
48:
48: NOTE 4 [file unknown]:
48: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
48:
48: Cleaning up constraints and constant bonded interactions with virtual sites
48: Removed 18 Angles with virtual sites, 21 left
48: Removed 10 Proper Dih.s with virtual sites, 44 left
48: Converted 15 Constraints with virtual sites to connections, 7 left
48: Number of degrees of freedom in T-Coupling group System is 23.00
48:
48: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 5 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 1.06800e+03 on atom 28
48: F-Norm = 4.26922e+02
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -1.69410778678185e+02
48: Maximum force = 2.18225948474048e+02 on atom 17
48: Norm of force = 7.92068036537643e+01
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (82 ms)
48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (6186 ms total)
48:
48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents converged to Fmax < 10 in 1 steps
48: Potential Energy = -9.74257075835450e-01
48: Maximum force = 4.01322929015108e+00 on atom 3
48: Norm of force = 1.63839399694368e+00
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (26 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 4.01323e+00 on atom 3
48: F-Norm = 1.63839e+00
48:
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
48: Potential Energy = -9.90642313893957e-01
48: Maximum force = 2.57812909491105e+00 on atom 3
48: Norm of force = 1.05251679559258e+00
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (27 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48:
48: There was 1 warning
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (13 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 3.19395484891518e+02
48: Maximum force = 9.97041707197910e+03 on atom 9
48: Norm of force = 4.62274878665467e+03
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (461 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 2.41672e+04 on atom 10
48: F-Norm = 1.19357e+04
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 1.56258793899479e+02
48: Maximum force = 7.50181017480397e+03 on atom 9
48: Norm of force = 3.61390332564874e+03
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (463 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48:
48: There was 1 warning
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (445 ms)
48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1435 ms total)
48:
48: [----------] Global test environment tear-down
48: [==========] 22 tests from 7 test cases ran. (8451 ms total)
48: [ PASSED ] 22 tests.
48:
48: YOU HAVE 4 DISABLED TESTS
48:
48/54 Test #48: MdrunMpiTests ....................... Passed 8.48 sec
test 49
Start 49: MdrunMpiCoordinationTestsOneRank
49: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml"
49: Test timeout computed to be: 480
49: [==========] Running 27 tests from 3 test cases.
49: [----------] Global test environment set-up.
49: [----------] 1 test from BasicPropagators/PeriodicActionsTest
49: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.116 0.116 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.608 1.904
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.105 0.105 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.011 1.713
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.099 0.100 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.748 1.627
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.083 0.083 99.6
49: (ns/day) (hour/ns)
49: Performance: 17.665 1.359
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.077 0.077 99.6
49: (ns/day) (hour/ns)
49: Performance: 19.052 1.260
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.102 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.384 1.669
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (745 ms)
49: [----------] 1 test from BasicPropagators/PeriodicActionsTest (745 ms total)
49:
49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.092 0.092 99.7
49: (ns/day) (hour/ns)
49: Performance: 15.953 1.504
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.088 0.088 99.6
49: (ns/day) (hour/ns)
49: Performance: 16.622 1.444
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.108 0.108 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.599 1.765
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.108 0.108 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.601 1.765
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.102 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.382 1.669
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.102 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.359 1.671
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (741 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.092 0.093 99.7
49: (ns/day) (hour/ns)
49: Performance: 15.866 1.513
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.097 0.097 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.136 1.586
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.090 0.091 99.6
49: (ns/day) (hour/ns)
49: Performance: 16.202 1.481
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.090 0.090 99.6
49: (ns/day) (hour/ns)
49: Performance: 16.257 1.476
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.126 0.126 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.640 2.062
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.102 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.421 1.664
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (742 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.620 1.642
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.088 0.089 99.6
49: (ns/day) (hour/ns)
49: Performance: 16.582 1.447
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.090 0.090 99.6
49: (ns/day) (hour/ns)
49: Performance: 16.261 1.476
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.098 0.098 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.928 1.608
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.092 0.093 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.828 1.516
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.504 1.655
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (718 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.108 0.108 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.597 1.765
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.113 0.113 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.952 1.853
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.691 1.634
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.673 1.636
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.102 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.344 1.673
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.119 0.119 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.356 1.942
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (782 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.142 0.142 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.314 2.327
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.113 0.114 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.927 1.857
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.115 0.115 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.757 1.881
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.123 0.124 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.858 2.024
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.102 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.428 1.663
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.118 0.118 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.407 1.934
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (859 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.108 0.108 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.538 1.773
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.130 0.130 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.286 2.127
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.123 0.124 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.890 2.018
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.115 0.115 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.760 1.881
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.134 0.135 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.904 2.201
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.160 0.160 99.8
49: (ns/day) (hour/ns)
49: Performance: 9.186 2.613
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (916 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.141 0.142 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.361 2.316
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.138 0.139 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.591 2.266
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.116 0.116 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.608 1.904
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.676 1.635
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.111 0.111 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.225 1.815
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.119 0.119 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.311 1.949
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (866 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.159 0.159 99.8
49: (ns/day) (hour/ns)
49: Performance: 9.216 2.604
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.147 0.147 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.001 2.400
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.157 0.157 99.8
49: (ns/day) (hour/ns)
49: Performance: 9.330 2.572
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.149 0.149 99.8
49: (ns/day) (hour/ns)
49: Performance: 9.858 2.435
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.102 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.423 1.664
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.102 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.422 1.664
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (959 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.625 1.641
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.105 0.105 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.945 1.721
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.148 0.148 99.8
49: (ns/day) (hour/ns)
49: Performance: 9.894 2.426
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.157 0.157 99.7
49: (ns/day) (hour/ns)
49: Performance: 9.337 2.570
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.151 0.152 99.8
49: (ns/day) (hour/ns)
49: Performance: 9.684 2.478
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.341 1.799
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (916 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.630 1.640
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.088 0.089 99.7
49: (ns/day) (hour/ns)
49: Performance: 16.549 1.450
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.117 0.117 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.549 1.913
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.167 0.167 99.8
49: (ns/day) (hour/ns)
49: Performance: 8.801 2.727
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.111 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.255 1.811
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.086 0.086 99.6
49: (ns/day) (hour/ns)
49: Performance: 17.075 1.406
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (807 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.092 0.093 99.7
49: (ns/day) (hour/ns)
49: Performance: 15.878 1.512
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.105 0.105 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.971 1.718
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.099 0.099 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.826 1.619
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.107 0.108 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.662 1.757
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.102 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.392 1.668
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.102 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.413 1.665
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (750 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.108 0.109 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.511 1.776
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.105 0.105 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.935 1.722
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.107 0.107 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.693 1.753
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.115 0.116 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.704 1.889
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.324 1.801
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.110 0.110 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.343 1.799
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (800 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.8
49: (ns/day) (hour/ns)
49: Performance: 14.520 1.653
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.089 0.089 99.8
49: (ns/day) (hour/ns)
49: Performance: 16.435 1.460
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.093 0.093 99.8
49: (ns/day) (hour/ns)
49: Performance: 15.834 1.516
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.076 0.076 99.7
49: (ns/day) (hour/ns)
49: Performance: 19.319 1.242
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.078 0.079 99.8
49: (ns/day) (hour/ns)
49: Performance: 18.690 1.284
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.095 0.095 99.8
49: (ns/day) (hour/ns)
49: Performance: 15.434 1.555
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (666 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.109 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.434 1.787
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.097 0.097 99.7
49: (ns/day) (hour/ns)
49: Performance: 15.144 1.585
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.107 0.108 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.636 1.760
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.099 0.099 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.766 1.625
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.085 0.085 99.6
49: (ns/day) (hour/ns)
49: Performance: 17.219 1.394
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.102 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.374 1.670
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (742 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.093 0.093 99.8
49: (ns/day) (hour/ns)
49: Performance: 15.760 1.523
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.098 0.098 99.8
49: (ns/day) (hour/ns)
49: Performance: 15.020 1.598
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.8
49: (ns/day) (hour/ns)
49: Performance: 14.550 1.649
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.109 99.8
49: (ns/day) (hour/ns)
49: Performance: 13.472 1.781
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.103 0.103 99.8
49: (ns/day) (hour/ns)
49: Performance: 14.230 1.687
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.120 0.120 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.259 1.958
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (758 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.117 0.117 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.520 1.917
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.121 0.122 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.065 1.989
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.107 0.108 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.646 1.759
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.091 0.091 99.6
49: (ns/day) (hour/ns)
49: Performance: 16.164 1.485
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.127 0.127 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.549 2.078
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.127 0.127 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.539 2.080
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (834 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.101 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.605 1.643
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.105 0.106 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.921 1.724
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.092 0.092 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.964 1.503
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.661 1.637
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.078 0.078 99.6
49: (ns/day) (hour/ns)
49: Performance: 18.858 1.273
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.078 0.078 99.6
49: (ns/day) (hour/ns)
49: Performance: 18.863 1.272
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (691 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.076 0.076 99.6
49: (ns/day) (hour/ns)
49: Performance: 19.272 1.245
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.097 0.097 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.133 1.586
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.124 0.124 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.847 2.026
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.132 0.132 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.118 2.159
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.126 0.127 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.603 2.068
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.118 0.119 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.389 1.937
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (817 ms)
49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (14365 ms total)
49:
49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.109 0.109 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.461 1.783
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.091 0.092 99.6
49: (ns/day) (hour/ns)
49: Performance: 15.998 1.500
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.644 1.639
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.115 0.115 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.732 1.885
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.103 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.295 1.679
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.112 0.112 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.125 1.829
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (15765 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.100 0.100 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.616 1.642
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.123 0.124 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.883 2.020
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.128 0.128 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.479 2.091
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.117 0.118 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.497 1.920
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.113 0.113 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.947 1.854
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.124 0.124 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.804 2.033
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (15807 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.126 0.126 99.8
49: (ns/day) (hour/ns)
49: Performance: 11.655 2.059
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.101 0.101 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.542 1.650
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.124 0.124 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.834 2.028
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.123 0.123 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.949 2.009
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.102 0.102 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.375 1.670
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.098 0.098 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.912 1.609
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (15780 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.119 0.119 99.7
49: (ns/day) (hour/ns)
49: Performance: 12.334 1.946
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.123 0.123 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.920 2.013
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.124 0.124 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.847 2.026
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.134 0.134 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.927 2.196
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.143 0.143 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.279 2.335
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.145 0.145 99.7
49: (ns/day) (hour/ns)
49: Performance: 10.108 2.374
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (15898 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.108 0.108 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.616 1.763
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.131 0.131 99.8
49: (ns/day) (hour/ns)
49: Performance: 11.209 2.141
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.132 0.132 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.118 2.159
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.126 0.126 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.636 2.063
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.104 0.105 99.7
49: (ns/day) (hour/ns)
49: Performance: 14.025 1.711
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.123 0.123 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.894 2.018
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (15814 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.125 0.125 99.7
49: (ns/day) (hour/ns)
49: Performance: 11.764 2.040
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.106 0.106 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.868 1.731
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.108 0.109 99.6
49: (ns/day) (hour/ns)
49: Performance: 13.529 1.774
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.112 0.112 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.109 1.831
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.103 0.103 99.6
49: (ns/day) (hour/ns)
49: Performance: 14.226 1.687
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.111 0.112 99.7
49: (ns/day) (hour/ns)
49: Performance: 13.154 1.825
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (15773 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.121 0.121 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.150 1.975
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.096 0.096 99.8
49: (ns/day) (hour/ns)
49: Performance: 15.236 1.575
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.123 0.123 99.8
49: (ns/day) (hour/ns)
49: Performance: 11.957 2.007
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.116 0.116 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.657 1.896
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.143 0.143 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.240 2.344
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.162 0.162 99.9
49: (ns/day) (hour/ns)
49: Performance: 9.060 2.649
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (15847 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.146 0.147 99.9
49: (ns/day) (hour/ns)
49: Performance: 10.019 2.395
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.141 0.142 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.368 2.315
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.143 0.143 99.8
49: (ns/day) (hour/ns)
49: Performance: 10.268 2.337
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.132 0.133 99.8
49: (ns/day) (hour/ns)
49: Performance: 11.069 2.168
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.119 0.120 99.8
49: (ns/day) (hour/ns)
49: Performance: 12.288 1.953
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: NOTE: Thread affinity was not set.
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.126 0.126 99.8
49: (ns/day) (hour/ns)
49: Performance: 11.671 2.056
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (15897 ms)
49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (126582 ms total)
49:
49: [----------] Global test environment tear-down
49: [==========] 27 tests from 3 test cases ran. (141692 ms total)
49: [ PASSED ] 27 tests.
49/54 Test #49: MdrunMpiCoordinationTestsOneRank .... Passed 141.72 sec
test 50
Start 50: MdrunMpiCoordinationTestsTwoRanks
50: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-coordination-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationTestsTwoRanks.xml"
50: Test timeout computed to be: 480
50: [==========] Running 27 tests from 3 test cases.
50: [----------] Global test environment set-up.
50: [----------] 1 test from BasicPropagators/PeriodicActionsTest
50: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.202 0.102 199.1
50: (ns/day) (hour/ns)
50: Performance: 14.443 1.662
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.186 0.094 198.9
50: (ns/day) (hour/ns)
50: Performance: 15.686 1.530
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.194 0.097 198.9
50: (ns/day) (hour/ns)
50: Performance: 15.073 1.592
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.261 0.131 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.216 2.140
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.250 0.125 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.711 2.049
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.249 0.125 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.737 2.045
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (848 ms)
50: [----------] 1 test from BasicPropagators/PeriodicActionsTest (848 ms total)
50:
50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.181 0.091 199.0
50: (ns/day) (hour/ns)
50: Performance: 16.133 1.488
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.187 0.094 198.9
50: (ns/day) (hour/ns)
50: Performance: 15.594 1.539
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.194 0.098 198.9
50: (ns/day) (hour/ns)
50: Performance: 15.058 1.594
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.194 0.098 198.9
50: (ns/day) (hour/ns)
50: Performance: 15.037 1.596
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.232 0.117 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.574 1.909
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.248 0.125 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.785 2.037
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (775 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.262 0.132 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.147 2.153
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.253 0.127 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.540 2.080
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.208 0.105 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.038 1.710
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.208 0.105 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.028 1.711
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.231 0.116 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.668 1.894
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.264 0.133 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.063 2.169
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (875 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.278 0.139 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.530 2.279
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.270 0.136 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.838 2.214
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.224 0.113 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.029 1.842
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.208 0.104 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.065 1.706
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.230 0.116 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.680 1.893
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.214 0.108 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.659 1.757
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (874 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.196 0.099 199.0
50: (ns/day) (hour/ns)
50: Performance: 14.905 1.610
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.254 0.128 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.513 2.085
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.261 0.131 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.228 2.138
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.260 0.131 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.243 2.135
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.199 0.100 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.646 1.639
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.199 0.100 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.666 1.636
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (841 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.197 0.099 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.808 1.621
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.253 0.127 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.538 2.080
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.257 0.129 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.384 2.108
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.475 0.238 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.167 3.892
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.230 0.115 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.732 1.885
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.249 0.125 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.728 2.046
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (994 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.275 0.138 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.646 2.254
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.254 0.127 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.531 2.081
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.241 0.121 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.126 1.979
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.239 0.120 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.213 1.965
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.229 0.115 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.760 1.881
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.213 0.107 198.8
50: (ns/day) (hour/ns)
50: Performance: 13.680 1.754
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (890 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.179 0.090 198.9
50: (ns/day) (hour/ns)
50: Performance: 16.298 1.473
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.137 0.069 198.4
50: (ns/day) (hour/ns)
50: Performance: 21.197 1.132
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.176 0.089 198.8
50: (ns/day) (hour/ns)
50: Performance: 16.552 1.450
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.159 0.080 198.3
50: (ns/day) (hour/ns)
50: Performance: 18.269 1.314
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.182 0.092 198.8
50: (ns/day) (hour/ns)
50: Performance: 16.025 1.498
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.182 0.091 198.8
50: (ns/day) (hour/ns)
50: Performance: 16.055 1.495
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (666 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.214 0.107 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.666 1.756
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.204 0.102 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.344 1.673
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.226 0.113 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.957 1.852
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.225 0.113 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.961 1.852
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.231 0.116 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.643 1.898
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.148 0.075 198.4
50: (ns/day) (hour/ns)
50: Performance: 19.688 1.219
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (783 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.146 0.074 198.5
50: (ns/day) (hour/ns)
50: Performance: 19.944 1.203
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.170 0.086 198.8
50: (ns/day) (hour/ns)
50: Performance: 17.154 1.399
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.191 0.096 198.8
50: (ns/day) (hour/ns)
50: Performance: 15.264 1.572
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.208 0.105 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.055 1.708
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.246 0.124 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.863 2.023
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.196 0.099 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.884 1.612
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (742 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.195 0.098 199.0
50: (ns/day) (hour/ns)
50: Performance: 14.969 1.603
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.170 0.085 198.8
50: (ns/day) (hour/ns)
50: Performance: 17.196 1.396
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.159 0.080 198.7
50: (ns/day) (hour/ns)
50: Performance: 18.313 1.311
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.144 0.072 198.5
50: (ns/day) (hour/ns)
50: Performance: 20.301 1.182
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.165 0.083 198.7
50: (ns/day) (hour/ns)
50: Performance: 17.662 1.359
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.182 0.091 198.8
50: (ns/day) (hour/ns)
50: Performance: 16.065 1.494
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (666 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.263 0.132 199.2
50: (ns/day) (hour/ns)
50: Performance: 11.112 2.160
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.170 0.085 198.7
50: (ns/day) (hour/ns)
50: Performance: 17.201 1.395
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.191 0.096 198.8
50: (ns/day) (hour/ns)
50: Performance: 15.276 1.571
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.175 0.088 198.7
50: (ns/day) (hour/ns)
50: Performance: 16.694 1.438
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.164 0.082 198.6
50: (ns/day) (hour/ns)
50: Performance: 17.818 1.347
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.164 0.083 198.6
50: (ns/day) (hour/ns)
50: Performance: 17.780 1.350
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (726 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.212 0.107 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.783 1.741
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.203 0.102 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.408 1.666
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.224 0.113 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.043 1.840
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.274 0.137 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.686 2.246
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.196 0.099 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.875 1.613
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.197 0.099 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.856 1.616
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (816 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.148 0.075 198.5
50: (ns/day) (hour/ns)
50: Performance: 19.650 1.221
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.189 0.095 198.8
50: (ns/day) (hour/ns)
50: Performance: 15.460 1.552
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.196 0.098 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.918 1.609
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.212 0.107 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.758 1.744
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.201 0.101 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.514 1.654
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.267 0.134 199.2
50: (ns/day) (hour/ns)
50: Performance: 10.949 2.192
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (758 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.179 0.090 198.8
50: (ns/day) (hour/ns)
50: Performance: 16.295 1.473
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.203 0.102 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.379 1.669
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.207 0.104 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.082 1.704
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.225 0.113 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.006 1.845
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.197 0.099 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.815 1.620
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.196 0.099 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.889 1.612
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (767 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.266 0.134 198.9
50: (ns/day) (hour/ns)
50: Performance: 10.984 2.185
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.183 0.092 198.8
50: (ns/day) (hour/ns)
50: Performance: 15.955 1.504
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.195 0.098 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.974 1.603
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.195 0.098 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.945 1.606
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.201 0.101 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.566 1.648
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.184 0.092 198.7
50: (ns/day) (hour/ns)
50: Performance: 15.888 1.511
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (766 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.162 0.082 198.7
50: (ns/day) (hour/ns)
50: Performance: 18.020 1.332
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.186 0.094 198.7
50: (ns/day) (hour/ns)
50: Performance: 15.669 1.532
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.191 0.096 198.8
50: (ns/day) (hour/ns)
50: Performance: 15.264 1.572
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.241 0.121 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.126 1.979
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.230 0.116 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.688 1.892
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.214 0.108 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.653 1.758
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (775 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.212 0.106 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.821 1.736
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.169 0.085 198.7
50: (ns/day) (hour/ns)
50: Performance: 17.286 1.388
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.158 0.080 198.6
50: (ns/day) (hour/ns)
50: Performance: 18.407 1.304
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.193 0.097 198.9
50: (ns/day) (hour/ns)
50: Performance: 15.115 1.588
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.182 0.091 198.8
50: (ns/day) (hour/ns)
50: Performance: 16.065 1.494
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.182 0.091 198.8
50: (ns/day) (hour/ns)
50: Performance: 16.074 1.493
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (707 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.213 0.107 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.742 1.747
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.203 0.102 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.404 1.666
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.207 0.104 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.121 1.700
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.224 0.112 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.064 1.837
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.197 0.099 198.7
50: (ns/day) (hour/ns)
50: Performance: 14.814 1.620
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.213 0.107 198.8
50: (ns/day) (hour/ns)
50: Performance: 13.689 1.753
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (792 ms)
50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (14216 ms total)
50:
50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.180 0.090 198.9
50: (ns/day) (hour/ns)
50: Performance: 16.232 1.479
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.202 0.102 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.462 1.660
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.228 0.115 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.822 1.872
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.220 0.110 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.306 1.804
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.207 0.104 199.0
50: (ns/day) (hour/ns)
50: Performance: 14.111 1.701
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.217 0.109 199.0
50: (ns/day) (hour/ns)
50: Performance: 13.449 1.785
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (15848 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.226 0.114 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.927 1.857
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.214 0.108 198.8
50: (ns/day) (hour/ns)
50: Performance: 13.632 1.761
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.237 0.119 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.319 1.948
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.249 0.125 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.737 2.045
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.219 0.110 198.7
50: (ns/day) (hour/ns)
50: Performance: 13.347 1.798
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.204 0.103 198.7
50: (ns/day) (hour/ns)
50: Performance: 14.309 1.677
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (15907 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.234 0.118 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.475 1.924
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.231 0.116 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.667 1.895
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.223 0.112 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.118 1.830
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.241 0.121 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.107 1.982
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.216 0.108 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.553 1.771
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.212 0.107 198.9
50: (ns/day) (hour/ns)
50: Performance: 13.751 1.745
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (15847 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.209 0.105 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.006 1.714
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.242 0.122 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.082 1.987
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.265 0.133 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.047 2.173
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.231 0.116 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.651 1.897
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.246 0.124 198.9
50: (ns/day) (hour/ns)
50: Performance: 11.857 2.024
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.215 0.108 198.8
50: (ns/day) (hour/ns)
50: Performance: 13.576 1.768
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (15907 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.223 0.112 199.1
50: (ns/day) (hour/ns)
50: Performance: 13.132 1.828
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.201 0.101 198.9
50: (ns/day) (hour/ns)
50: Performance: 14.541 1.651
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.191 0.096 198.8
50: (ns/day) (hour/ns)
50: Performance: 15.305 1.568
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.261 0.131 199.1
50: (ns/day) (hour/ns)
50: Performance: 11.217 2.140
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.230 0.116 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.693 1.891
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.242 0.122 199.1
50: (ns/day) (hour/ns)
50: Performance: 12.062 1.990
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (15855 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.319 0.160 199.3
50: (ns/day) (hour/ns)
50: Performance: 9.189 2.612
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.267 0.134 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.945 2.193
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.235 0.118 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.448 1.928
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.274 0.138 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.665 2.250
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.249 0.125 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.735 2.045
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.274 0.137 199.1
50: (ns/day) (hour/ns)
50: Performance: 10.691 2.245
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (15998 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.227 0.114 198.8
50: (ns/day) (hour/ns)
50: Performance: 12.884 1.863
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.229 0.115 199.0
50: (ns/day) (hour/ns)
50: Performance: 12.751 1.882
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.229 0.115 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.737 1.884
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.204 0.103 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.283 1.680
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.209 0.105 198.8
50: (ns/day) (hour/ns)
50: Performance: 13.986 1.716
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.198 0.100 198.8
50: (ns/day) (hour/ns)
50: Performance: 14.713 1.631
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (15823 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.257 0.129 199.0
50: (ns/day) (hour/ns)
50: Performance: 11.377 2.110
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.218 0.110 198.8
50: (ns/day) (hour/ns)
50: Performance: 13.390 1.792
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.233 0.117 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.522 1.917
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.239 0.120 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.228 1.963
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.254 0.128 198.8
50: (ns/day) (hour/ns)
50: Performance: 11.498 2.087
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.241 0.121 198.9
50: (ns/day) (hour/ns)
50: Performance: 12.105 1.983
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (15906 ms)
50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (127091 ms total)
50:
50: [----------] Global test environment tear-down
50: [==========] 27 tests from 3 test cases ran. (142155 ms total)
50: [ PASSED ] 27 tests.
50/54 Test #50: MdrunMpiCoordinationTestsTwoRanks ... Passed 142.19 sec
test 51
Start 51: GmxapiExternalInterfaceTests
51: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiExternalInterfaceTests.xml"
51: Test timeout computed to be: 600
51: [==========] Running 9 tests from 2 test cases.
51: [----------] Global test environment set-up.
51: [----------] 8 tests from GmxApiTest
51: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
51: Setting the LD random seed to 2076432338
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 2 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.248 0.124 199.4
51: (ns/day) (hour/ns)
51: Performance: 4.079 5.884
51: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (1210 ms)
51: [ RUN ] GmxApiTest.SystemConstruction
51: Setting the LD random seed to 466997687
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51: [ OK ] GmxApiTest.SystemConstruction (2529 ms)
51: [ RUN ] GmxApiTest.SaneVersionComparisons
51: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms)
51: [ RUN ] GmxApiTest.VersionNamed0_1_Features
51: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms)
51: [ RUN ] GmxApiTest.RunnerBasicMD
51: Setting the LD random seed to 2105807194
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 2 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.277 0.139 199.4
51: (ns/day) (hour/ns)
51: Performance: 3.649 6.576
51: [ OK ] GmxApiTest.RunnerBasicMD (2671 ms)
51: [ RUN ] GmxApiTest.RunnerReinitialize
51: Setting the LD random seed to -2066434177
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 20 steps, 0.0 ps.
51:
51:
51: Received the remote INT/TERM signal, stopping within 50 steps
51:
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.320 0.160 199.5
51: (ns/day) (hour/ns)
51: Performance: 22.117 1.085
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 20 steps, 0.0 ps.
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.224 0.113 199.2
51: (ns/day) (hour/ns)
51: Performance: 31.458 0.763
51: [ OK ] GmxApiTest.RunnerReinitialize (2816 ms)
51: [ RUN ] GmxApiTest.RunnerContinuedMD
51: Setting the LD random seed to 1550886728
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 10 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.286 0.143 199.5
51: (ns/day) (hour/ns)
51: Performance: 12.952 1.853
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
51: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 20 steps, 0.0 ps.
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.225 0.113 199.2
51: (ns/day) (hour/ns)
51: Performance: 31.400 0.764
51: [ OK ] GmxApiTest.RunnerContinuedMD (2792 ms)
51: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
51: Setting the LD random seed to 2133820213
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
51: Changing nstlist from 10 to 1, rlist from 1.041 to 1
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 1 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.267 0.134 199.5
51: (ns/day) (hour/ns)
51: Performance: 2.525 9.503
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
51: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
51: Changing nstlist from 10 to 1, rlist from 1.041 to 1
51:
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 2 steps, 0.0 ps.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.258 0.129 199.3
51: (ns/day) (hour/ns)
51: Performance: 2.612 9.187
51: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (2815 ms)
51: [----------] 8 tests from GmxApiTest (14833 ms total)
51:
51: [----------] 1 test from GmxApiBasicTest
51: [ RUN ] GmxApiBasicTest.Status
51: [ OK ] GmxApiBasicTest.Status (0 ms)
51: [----------] 1 test from GmxApiBasicTest (0 ms total)
51:
51: [----------] Global test environment tear-down
51: [==========] 9 tests from 2 test cases ran. (14834 ms total)
51: [ PASSED ] 9 tests.
51/54 Test #51: GmxapiExternalInterfaceTests ........ Passed 14.86 sec
test 52
Start 52: GmxapiMpiTests
52: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxapi-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiMpiTests.xml"
52: Test timeout computed to be: 600
52: [==========] Running 9 tests from 2 test cases.
52: [----------] Global test environment set-up.
52: [----------] 8 tests from GmxApiTest
52: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
52: Setting the LD random seed to 1064993751
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 2 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.294 0.147 199.5
52: (ns/day) (hour/ns)
52: Performance: 3.439 6.978
52: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (1238 ms)
52: [ RUN ] GmxApiTest.SystemConstruction
52: Setting the LD random seed to 1790136438
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52: [ OK ] GmxApiTest.SystemConstruction (2514 ms)
52: [ RUN ] GmxApiTest.SaneVersionComparisons
52: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms)
52: [ RUN ] GmxApiTest.VersionNamed0_1_Features
52: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms)
52: [ RUN ] GmxApiTest.RunnerBasicMD
52: Setting the LD random seed to -568287940
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 2 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.221 0.111 199.4
52: (ns/day) (hour/ns)
52: Performance: 4.574 5.247
52: [ OK ] GmxApiTest.RunnerBasicMD (2626 ms)
52: [ RUN ] GmxApiTest.RunnerReinitialize
52: Setting the LD random seed to 733369283
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 20 steps, 0.0 ps.
52:
52:
52: Received the remote INT/TERM signal, stopping within 50 steps
52:
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.305 0.153 199.5
52: (ns/day) (hour/ns)
52: Performance: 23.164 1.036
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 20 steps, 0.0 ps.
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.325 0.163 199.5
52: (ns/day) (hour/ns)
52: Performance: 21.777 1.102
52: [ OK ] GmxApiTest.RunnerReinitialize (2841 ms)
52: [ RUN ] GmxApiTest.RunnerContinuedMD
52: Setting the LD random seed to 1439849707
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 10 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.329 0.165 199.5
52: (ns/day) (hour/ns)
52: Performance: 11.270 2.130
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
52: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 20 steps, 0.0 ps.
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.275 0.138 199.4
52: (ns/day) (hour/ns)
52: Performance: 25.718 0.933
52: [ OK ] GmxApiTest.RunnerContinuedMD (2833 ms)
52: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
52: Setting the LD random seed to -1385163083
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
52: Changing nstlist from 10 to 1, rlist from 1.041 to 1
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 1 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.269 0.135 199.5
52: (ns/day) (hour/ns)
52: Performance: 2.502 9.591
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.4-Raspbian-2020.4-2 (double precision)
52: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
52: Changing nstlist from 10 to 1, rlist from 1.041 to 1
52:
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 2 steps, 0.0 ps.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.225 0.113 199.3
52: (ns/day) (hour/ns)
52: Performance: 2.993 8.020
52: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (2774 ms)
52: [----------] 8 tests from GmxApiTest (14827 ms total)
52:
52: [----------] 1 test from GmxApiBasicTest
52: [ RUN ] GmxApiBasicTest.Status
52: [ OK ] GmxApiBasicTest.Status (0 ms)
52: [----------] 1 test from GmxApiBasicTest (0 ms total)
52:
52: [----------] Global test environment tear-down
52: [==========] 9 tests from 2 test cases ran. (14827 ms total)
52: [ PASSED ] 9 tests.
52/54 Test #52: GmxapiMpiTests ...................... Passed 14.85 sec
test 53
Start 53: GmxapiInternalInterfaceTests
53: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiInternalInterfaceTests.xml"
53: Test timeout computed to be: 600
53: [==========] Running 2 tests from 1 test case.
53: [----------] Global test environment set-up.
53: [----------] 2 tests from GmxApiTest
53: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
53: Setting the LD random seed to 1122243506
53: Generated 331705 of the 331705 non-bonded parameter combinations
53: Generating 1-4 interactions: fudge = 0.5
53: Generated 331705 of the 331705 1-4 parameter combinations
53: Excluding 2 bonded neighbours molecule type 'SOL'
53: Excluding 3 bonded neighbours molecule type 'methane'
53:
53: NOTE 1 [file spc_and_methane.top, line 33]:
53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
53: the time step of 2.0e-03 ps.
53: Maybe you forgot to change the constraints mdp option.
53:
53: Number of degrees of freedom in T-Coupling group System is 18.00
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53: This run will generate roughly 0 Mb of data
53: [ OK ] GmxApiTest.BuildApiWorkflowImpl (1040 ms)
53: [ RUN ] GmxApiTest.CreateApiWorkflow
53: Setting the LD random seed to 763854429
53: Generated 331705 of the 331705 non-bonded parameter combinations
53: Generating 1-4 interactions: fudge = 0.5
53: Generated 331705 of the 331705 1-4 parameter combinations
53: Excluding 2 bonded neighbours molecule type 'SOL'
53: Excluding 3 bonded neighbours molecule type 'methane'
53:
53: NOTE 1 [file spc_and_methane.top, line 33]:
53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
53: the time step of 2.0e-03 ps.
53: Maybe you forgot to change the constraints mdp option.
53:
53: Number of degrees of freedom in T-Coupling group System is 18.00
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53: This run will generate roughly 0 Mb of data
53: [ OK ] GmxApiTest.CreateApiWorkflow (1069 ms)
53: [----------] 2 tests from GmxApiTest (2109 ms total)
53:
53: [----------] Global test environment tear-down
53: [==========] 2 tests from 1 test case ran. (2110 ms total)
53: [ PASSED ] 2 tests.
53/54 Test #53: GmxapiInternalInterfaceTests ........ Passed 2.14 sec
test 54
Start 54: GmxapiInternalsMpiTests
54: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/workflow-details-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiInternalsMpiTests.xml"
54: Test timeout computed to be: 600
54: [==========] Running 2 tests from 1 test case.
54: [----------] Global test environment set-up.
54: [----------] 2 tests from GmxApiTest
54: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
54: Setting the LD random seed to 316291362
54: Generated 331705 of the 331705 non-bonded parameter combinations
54: Generating 1-4 interactions: fudge = 0.5
54: Generated 331705 of the 331705 1-4 parameter combinations
54: Excluding 2 bonded neighbours molecule type 'SOL'
54: Excluding 3 bonded neighbours molecule type 'methane'
54:
54: NOTE 1 [file spc_and_methane.top, line 33]:
54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
54: the time step of 2.0e-03 ps.
54: Maybe you forgot to change the constraints mdp option.
54:
54: Number of degrees of freedom in T-Coupling group System is 18.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54: This run will generate roughly 0 Mb of data
54: [ OK ] GmxApiTest.BuildApiWorkflowImpl (1037 ms)
54: [ RUN ] GmxApiTest.CreateApiWorkflow
54: Setting the LD random seed to 547973618
54: Generated 331705 of the 331705 non-bonded parameter combinations
54: Generating 1-4 interactions: fudge = 0.5
54: Generated 331705 of the 331705 1-4 parameter combinations
54: Excluding 2 bonded neighbours molecule type 'SOL'
54: Excluding 3 bonded neighbours molecule type 'methane'
54:
54: NOTE 1 [file spc_and_methane.top, line 33]:
54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
54: the time step of 2.0e-03 ps.
54: Maybe you forgot to change the constraints mdp option.
54:
54: Number of degrees of freedom in T-Coupling group System is 18.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54: This run will generate roughly 0 Mb of data
54: [ OK ] GmxApiTest.CreateApiWorkflow (1064 ms)
54: [----------] 2 tests from GmxApiTest (2101 ms total)
54:
54: [----------] Global test environment tear-down
54: [==========] 2 tests from 1 test case ran. (2101 ms total)
54: [ PASSED ] 2 tests.
54/54 Test #54: GmxapiInternalsMpiTests ............. Passed 2.13 sec
100% tests passed, 0 tests failed out of 54
Label Time Summary:
GTest = 448.72 sec*proc (54 tests)
IntegrationTest = 136.94 sec*proc (12 tests)
MpiTest = 309.50 sec*proc (8 tests)
SlowTest = 283.91 sec*proc (2 tests)
UnitTest = 27.87 sec*proc (40 tests)
Total Test time (real) = 448.94 sec
touch build-basic
dh_testdir
/usr/bin/make -j4 -C build/mpich
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/mpich --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/mpich/CMakeFiles /<<PKGBUILDDIR>>/build/mpich//CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
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cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/selection /<<PKGBUILDDIR>>/build/mpich/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.4-Raspbian-2020.4-2 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/mpich/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/mpich/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2020.4-2 -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoRelease.cmake
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Scanning dependencies of target thread_mpi
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
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Scanning dependencies of target scanner
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
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Scanning dependencies of target linearalgebra
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
Scanning dependencies of target modularsimulator
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 2%] Built target linearalgebra
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 2%] Built target scanner
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/programs /<<PKGBUILDDIR>>/build/mpich/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 4%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 6%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 9%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/mpich/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetree.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreemdpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/logger.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/loggerbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/mpiinplacebuffers.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/niceheader.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
2280 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:103:16: warning: ignoring return value of 'char* getenv(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
103 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp: In member function 'void gmx::UpdateConstrainCuda::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
70 | void UpdateConstrainCuda::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingparameters.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<float> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:104:16: warning: ignoring return value of 'char* getenv(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
104 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_testutils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1280:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1280 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1281 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1282 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1283 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<float> >, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:114:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
114 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/vmdio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionbehavior.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selelem.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selhelp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selmethod.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selvalue.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_compare.cpp
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/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun.dir/mdrun_main.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/mdrun_mpi.mpich ../../lib/libgromacs_mdrun_mpi.mpich.a /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
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cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
Scanning dependencies of target release-version-info
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cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.4-Raspbian-2020.4-2 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/mpich-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/mpich-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2020.4-2 -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoRelease.cmake
Scanning dependencies of target scanner
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Scanning dependencies of target thread_mpi
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/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 0%] Built target release-version-info
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
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/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 2%] Built target lmfit_objlib
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
Scanning dependencies of target modularsimulator
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp: In member function 'void gmx::CheckpointHelper::writeCheckpoint(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp:129:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
129 | mdoutf_write_to_trajectory_files(fplog_, cr_, trajectoryElement_->outf_, MDOF_CPT,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
130 | globalNumAtoms_, step, time, localStateInstance_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
131 | state_global_, observablesHistory_, ArrayRef<RVec>());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 2%] Built target linearalgebra
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/programs /<<PKGBUILDDIR>>/build/mpich-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 2%] Built target scanner
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 4%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In static member function 'static _Res std::_Function_handler<_Res(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Res = void; _Functor = gmx::FreeEnergyPerturbationElement::scheduleTask(gmx::Step, gmx::Time, const RegisterRunFunctionPtr&)::<lambda()>; _ArgTypes = {}]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:86:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
86 | setCurrentLambdasLocal(step, inputrec_->fepvals, lambda0_.data(), lambda_, currentFEPState_);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In constructor 'gmx::FreeEnergyPerturbationElement::FreeEnergyPerturbationElement(FILE*, const t_inputrec*, gmx::MDAtoms*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:68:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
68 | initialize_lambdas(fplog_, *inputrec_, true, ¤tFEPState_, lambda_, lambda0_.data());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In member function 'void gmx::FreeEnergyPerturbationElement::updateLambdas(gmx::Step)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:86:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
86 | setCurrentLambdasLocal(step, inputrec_->fepvals, lambda0_.data(), lambda_, currentFEPState_);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp: In member function 'void gmx::ForceElement::run(gmx::Step, gmx::Time, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp:159:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
159 | do_force(fplog_, cr_, ms, inputrec_, awh, enforcedRotation_, imdSession_, pull_work_, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
160 | nrnb_, wcycle_, localTopology_, box, x, hist, forces, force_vir, mdAtoms_->mdatoms(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
161 | energyElement_->enerdata(), fcd_, lambda, graph, fr_, runScheduleWork_, vsite_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
162 | energyElement_->muTot(), time, ed, static_cast<int>(flags), ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp: In member function 'void gmx::EnergyElement::doStep(gmx::Time, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | sum_dhdl(enerd_, freeEnergyPerturbationElement_->constLambdaView(), *inputrec_->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp: In constructor 'gmx::ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int, int, real, gmx::Step, gmx::ArrayRef<double [3]>, gmx::PropagatorCallbackPtr, gmx::StatePropagatorData*, gmx::EnergyElement*, FILE*, const t_inputrec*, const gmx::MDAtoms*, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:62:1: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
62 | ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int nstpcouple,
| ^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp: In member function 'void gmx::PmeLoadBalanceHelper::run(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp:107:19: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
107 | pme_loadbal_do(pme_loadbal_, cr_, (isVerbose_ && MASTER(cr_)) ? stderr : nullptr, fplog_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
108 | mdlog_, *inputrec_, fr_, statePropagatorData_->constBox(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
109 | statePropagatorData_->constPositionsView().paddedArrayRef(), wcycle_, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
110 | step - inputrec_->init_step, &bPMETunePrinting_, false);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp: In member function 'void gmx::ShellFCElement::run(gmx::Step, gmx::Time, bool, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp:185:24: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
185 | relax_shell_flexcon(fplog_, cr_, ms, isVerbose_, enforcedRotation_, step, inputrec_, imdSession_,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
186 | pull_work_, isNSStep, static_cast<int>(flags), localTopology_, constr_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
187 | energyElement_->enerdata(), fcd_, statePropagatorData_->localNumAtoms(), x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
188 | v, box, lambda, hist, forces, force_vir, mdAtoms_->mdatoms(), nrnb_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
189 | wcycle_, graph, shellfc_, fr_, runScheduleWork_, time,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
190 | energyElement_->muTot(), vsite_, ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::_ZN3gmx19StatePropagatorData24trajectoryWriterTeardownEP10gmx_mdoutf.part.0(gmx_mdoutf*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:464:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
464 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:466:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
466 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 6%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::write(gmx_mdoutf_t, gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:411:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
411 | mdoutf_write_to_trajectory_files(fplog_, cr_, outf, static_cast<int>(mdof_flags),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
412 | totalNumAtoms_, currentStep, currentTime,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
413 | localStateBackup_.get(), globalState_, observablesHistory, f_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/isimulator.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp:44:
/usr/include/c++/10/bits/unique_ptr.h: In member function 'std::unique_ptr<gmx::ISimulatorElement> gmx::ModularSimulator::buildIntegrator(gmx::SignallerBuilder<gmx::NeighborSearchSignaller>*, gmx::SignallerBuilder<gmx::EnergySignaller>*, gmx::SignallerBuilder<gmx::LoggingSignaller>*, gmx::TrajectoryElementBuilder*, std::vector<gmx::ICheckpointHelperClient*>*, gmx::CheckBondedInteractionsCallbackPtr*, gmx::compat::not_null<gmx::StatePropagatorData*>, gmx::compat::not_null<gmx::EnergyElement*>, gmx::FreeEnergyPerturbationElement*, bool)':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::StatePropagatorData::setLocalState(std::unique_ptr<t_state>)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::StatePropagatorData::StatePropagatorData(int, FILE*, const t_commrec*, t_state*, int, int, int, int, bool, gmx::FreeEnergyPerturbationElement*, const gmx::TopologyHolder*, bool, bool, std::string, const t_inputrec*, const t_mdatoms*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp: In constructor 'gmx::VRescaleThermostat::VRescaleThermostat(int, int, bool, int64_t, int, double, const real*, const real*, const real*, gmx::EnergyElement*, gmx::ArrayRef<double>, gmx::PropagatorCallbackPtr, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp:59:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
59 | VRescaleThermostat::VRescaleThermostat(int nstcouple,
| ^~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 9%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/mpich-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetree.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreemdpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/logger.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/loggerbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/mpiinplacebuffers.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/niceheader.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/smalloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strdb.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function 'void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:1484:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1484 | void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t& nbat, gmx::ArrayRef<gmx::RVec> fshift)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp: In function 'void Nbnxm::setupAndRunInstance(const gmx::BenchmarkSystem&, const Nbnxm::KernelBenchOptions&, bool)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:222:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
222 | nbnxn_put_on_grid(nbv.get(), system.box, 0, lowerCorner, upperCorner, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
223 | { 0, int(system.coordinates.size()) }, atomDensity, atomInfo,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | system.coordinates, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Nbnxm::KernelBenchOptions&}; _Tp = Nbnxm::KernelBenchOptions; _Alloc = std::allocator<Nbnxm::KernelBenchOptions>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Nbnxm::KernelBenchOptions>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In function 'void Nbnxm::bench(int, const Nbnxm::KernelBenchOptions&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In function '_ZN5Nbnxm7GridSet9putOnGridEPA3_KdiPS1_S4_PKN3gmx15UpdateGroupsCogENS5_5RangeIiEEdNS5_8ArrayRefIKiEENSB_IKNS5_11BasicVectorIdEEEEiPSC_P16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:216:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
216 | Grid::calcColumnIndices(grid.dimensions(), updateGroupsCog, atomRange, x, ddZone, move, thread,
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
217 | nthread, gridSetData_.cells, gridWork_[thread].numAtomsPerColumn);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In member function 'void Nbnxm::GridSet::putOnGrid(const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:136:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
136 | void GridSet::putOnGrid(const matrix box,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:223:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
223 | grid.setCellIndices(ddZone, cellOffset, &gridSetData_, gridWork_, atomRange, atomInfo.data(), x,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | numAtomsMoved, nbat);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::fillCell(Nbnxm::GridSetData*, nbnxn_atomdata_t*, int, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, Nbnxm::BoundingBox*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:859:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
859 | void Grid::fillCell(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsCpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:987:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
987 | void Grid::sortColumnsCpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsGpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1050:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1050 | void Grid::sortColumnsGpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In function '_ZN5Nbnxm4Grid14setCellIndicesEiiPNS_11GridSetDataEN3gmx8ArrayRefINS_8GridWorkEEENS3_5RangeIiEEPKiNS4_IKNS3_11BasicVectorIdEEEEiP16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1409:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1409 | sortColumnsGpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1410 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1404:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1404 | sortColumnsCpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1405 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In static member function 'static void Nbnxm::Grid::calcColumnIndices(const Nbnxm::Grid::Dimensions&, const gmx::UpdateGroupsCog*, gmx::Range<int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, int, int, gmx::ArrayRef<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1172:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1172 | void Grid::calcColumnIndices(const Grid::Dimensions& gridDims,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp: In member function 'void nonbonded_verlet_t::dispatchNonbondedKernel(gmx::InteractionLocality, const interaction_const_t&, const gmx::StepWorkload&, int, const t_forcerec&, gmx_enerdata_t*, t_nrnb*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp:442:33: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
442 | nbnxn_kernel_gpu_ref(
| ~~~~~~~~~~~~~~~~~~~~^
443 | pairlistSet.gpuList(), nbat.get(), &ic, fr.shift_vec, stepWork, clearF,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
444 | nbat->out[0].f, nbat->out[0].fshift.data(), enerd->grpp.ener[egCOULSR].data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
445 | fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::setCellIndices(int, int, Nbnxm::GridSetData*, gmx::ArrayRef<Nbnxm::GridWork>, gmx::Range<int>, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1286 | void Grid::setCellIndices(int ddZone,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp: In function 'void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu*, const nbnxn_atomdata_t*, const interaction_const_t*, real (*)[3], const gmx::StepWorkload&, int, gmx::ArrayRef<double>, real*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
57 | void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu* nbl,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid(nonbonded_verlet_t*, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
57 | void nbnxn_put_on_grid(nonbonded_verlet_t* nb_verlet,
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:53:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.h:184:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
184 | gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
185 | atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*, const gmx_domdec_zones_t*, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:76:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
76 | void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t* nbv,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:53:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.h:184:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
184 | gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
185 | atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::convertCoordinates(gmx::AtomLocality, bool, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
126 | void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(gmx::AtomLocality, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:159:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
159 | void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::PinningPolicy}; _Tp = NbnxnPairlistGpu; _Alloc = std::allocator<NbnxnPairlistGpu>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<NbnxnPairlistGpu>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'PairlistSet::PairlistSet(gmx::InteractionLocality, const PairlistParams&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, const MPI_Comm*, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:232:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
232 | static void low_set_ddbox(int numPbcDimensions,
| ^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:278:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
278 | void set_ddbox(const gmx_domdec_t& dd,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
291 | low_set_ddbox(dd.unitCellInfo.npbcdim, dd.unitCellInfo.numBoundedDimensions, &dd.nc, box,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
292 | calculateUnboundedSize, xRef,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr, ddbox);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(const t_commrec&, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:302:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
302 | void set_ddbox_cr(const t_commrec& cr,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:311:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
311 | low_set_ddbox(ePBC2npbcdim(ir.ePBC), inputrec2nboundeddim(&ir), dd_nc, box, true, x, nullptr, ddbox);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, const t_state*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
228 | void dd_collect_vec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:291:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
291 | dd_collect_vec(dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:296:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
296 | dd_collect_vec(dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:301:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
301 | dd_collect_vec(dd, state_local, state_local->cg_p, globalCgpRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp: In function 'void distributeVec(gmx_domdec_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:143:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
143 | static void distributeVec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:143:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp: In function 'void distributeState(const gmx::MDLogger&, gmx_domdec_t*, const gmx_mtop_t&, t_state*, const gmx_ddbox_t&, t_state*, PaddedHostVector<gmx::BasicVector<double> >*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:259:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
259 | distributeVec(dd, DDMASTER(dd) ? state->x : gmx::ArrayRef<const gmx::RVec>(), state_local->x);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:259:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:259:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:263:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
263 | distributeVec(dd, DDMASTER(dd) ? state->v : gmx::ArrayRef<const gmx::RVec>(), state_local->v);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:263:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:263:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:267:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
267 | distributeVec(dd, DDMASTER(dd) ? state->cg_p : gmx::ArrayRef<const gmx::RVec>(), state_local->cg_p);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:267:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:267:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
118 | void ddSendrecv(const gmx_domdec_t* dd,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3156:17: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3156 | static gmx_bool test_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3166:14: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3166 | set_ddbox(*dd, false, box, true, x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool change_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3228:10: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3228 | gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp: In function 'DDGridSetup getDDGridSetup(const gmx::MDLogger&, const t_commrec*, int, const gmx::DomdecOptions&, const DDSettings&, const DDSystemInfo&, real, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:906:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
906 | DDGridSetup getDDGridSetup(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:934:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
934 | set_ddbox_cr(*cr, &numDomainsLegacyIvec, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:938:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
938 | set_ddbox_cr(*cr, nullptr, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::Impl::Impl(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3045:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3045 | DomainDecompositionBuilder::Impl::Impl(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2967:82: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2967 | gridSetupCellsizeLimit, mtop, ir, box, xGlobal, &ddbox);
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3091:92: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3091 | gridSetupCellsizeLimit, mtop_, ir_, box, xGlobal, &ddbox_);
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::DomainDecompositionBuilder(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3134:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3134 | DomainDecompositionBuilder::DomainDecompositionBuilder(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3143:95: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3143 | impl_(new Impl(mdlog, cr, options, mdrunOptions, prefer1DAnd1Pulse, mtop, ir, box, xGlobal))
| ^
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
531 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
595 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:272:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
272 | void dd_move_x(gmx_domdec_t* dd, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_wallcycle* wcycle)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
349 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ForceWithShiftForces*, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
424 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void dd_resize_state(t_state*, PaddedHostVector<gmx::BasicVector<double> >*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
253 | ddSendrecv(dd, d, dddirBackward, gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
254 | gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::scale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:65:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
65 | void ScaleCoordinates::Impl::scale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:75:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
75 | void ScaleCoordinates::Impl::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
97 | void ScaleCoordinates::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:102:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
102 | void ScaleCoordinates::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:104:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
104 | impl_->inverseIgnoringZeroScale(coordinates);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::Impl::transform(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:140:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
140 | void TranslateAndScale::Impl::transform(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:161:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
161 | void TranslateAndScale::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2104 | ddSendrecv<gmx::RVec>(dd, dim_ind, dddirBackward, work.positionBuffer, rvecBufferRef);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t&, const t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx_vsite_t*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2866:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2866 | set_ddbox(*dd, true, DDMASTER(dd) ? state_global->box : nullptr, true, xGlobal, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2907:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2907 | set_ddbox(*dd, bMasterState, state_local->box, true, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2928:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2928 | set_ddbox(*dd, bMasterState, state_local->box, bNStGlobalComm, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2946 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2947 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), state_local->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2970 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2971 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2972 | state_local->x);
| ~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3005:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3005 | nbnxn_put_on_grid(fr->nbv.get(), state_local->box, 0, comm->zones.size[0].bb_x0,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3006 | comm->zones.size[0].bb_x1, comm->updateGroupsCog.get(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3007 | { 0, dd->ncg_home }, comm->zones.dens_zone0, fr->cginfo, state_local->x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3008 | ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::index))[3]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:208:7: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
208 | rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n)
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'void initialize_lambdas(FILE*, const t_inputrec&, bool, int*, gmx::ArrayRef<double>, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:282:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
282 | void initialize_lambdas(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1394:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1394 | void put_atoms_in_box(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box_omp(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1454:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1454 | void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_unused int nth)
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1470:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1470 | void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(int, int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1527 | void put_atoms_in_compact_unitcell(int ePBC, int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_molecule_com_in_box(int, int, t_block*, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
289 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_residue_com_in_box(int, int, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
341 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp:53:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BaseEntry}; _Tp = BaseEntry; _Alloc = std::allocator<BaseEntry>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BaseEntry>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void readProperty(AtomProperty*, ResidueType*, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BaseEntry*, std::vector<BaseEntry> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp:52:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator<swap_group>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<swap_group>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 't_swap* init_swapcoords(FILE*, const t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const gmx::MdrunOptions&, gmx::StartingBehavior)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp:48:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator<edpar>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::unique_ptr<gmx::EssentialDynamics> ed_open(int, ObservablesHistory*, const char*, const char*, gmx::StartingBehavior, const gmx_output_env_t*, const t_commrec*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef<const gmx::BasicVector<double> >, const t_pbc&, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
949 | bool pullCheckPbcWithinGroup(const pull_t& pull,
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
2280 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp:106:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
106 | void BoxDeformation::apply(ArrayRef<RVec> x, matrix box, int64_t step)
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(const t_commrec*, t_state*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef<gmx::BasicVector<double> >, const real*, const real*, int, double*, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp:50:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
50 | void calc_mu(int start,
| ^~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator<VerletbufAtomtype>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VerletbufAtomtype>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<VerletbufAtomtype> getVerletBufferAtomtypes(const gmx_mtop_t&, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
60 | static void constr_recur(const t_blocka* at2con,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 't_blocka gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:826:10: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
826 | t_blocka make_at2con(const gmx_moltype_t& moltype,
| ^~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:107:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
107 | DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, real, const std::vector<bool>&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
810 | void andersen_tcoupl(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::DispersionCorrection(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>, const interaction_const_t&, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:520:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
520 | DispersionCorrection::DispersionCorrection(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:530:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
530 | topParams_(mtop, inputrec, useBuckingham, numAtomTypes, nonbondedForceParameters)
| ^
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp: In function 'void add_ebin_indexed(t_ebin*, int, gmx::ArrayRef<bool>, gmx::ArrayRef<const double>, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp:197:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
197 | void add_ebin_indexed(t_ebin* eb,
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function 'void sum_dhdl(gmx_enerdata_t*, gmx::ArrayRef<const double>, const t_lambda&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:92:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
92 | void sum_dhdl(gmx_enerdata_t* enerd, gmx::ArrayRef<const real> lambda, const t_lambda& fepvals)
| ^~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp: In function 'void do_force_lowlevel(t_forcerec*, const t_inputrec*, const t_idef*, const t_commrec*, const gmx_multisim_t*, t_nrnb*, gmx_wallcycle_t, const t_mdatoms*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ForceOutputs*, gmx_enerdata_t*, t_fcdata*, const real (*)[3], const real*, const t_graph*, const real (*)[3], const gmx::StepWorkload&, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
290 | status = gmx_pme_do(
| ~~~~~~~~~~^
291 | fr->pmedata,
| ~~~~~~~~~~~~
292 | gmx::constArrayRefFromArray(coordinates.unpaddedConstArrayRef().data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | md->homenr - fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~
294 | forceWithVirial.force_, md->chargeA, md->chargeB, md->sqrt_c6A,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
295 | md->sqrt_c6B, md->sigmaA, md->sigmaB, box, cr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
296 | DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
297 | DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0, nrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
298 | ewaldOutput.vir_q, ewaldOutput.vir_lj, &Vlr_q, &Vlr_lj,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
299 | lambda[efptCOUL], lambda[efptVDW], &ewaldOutput.dvdl[efptCOUL],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
300 | &ewaldOutput.dvdl[efptVDW], pme_flags);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
325 | gmx_pme_calc_energy(
| ~~~~~~~~~~~~~~~~~~~^
326 | fr->pmedata,
| ~~~~~~~~~~~~
327 | coordinates.unpaddedConstArrayRef().subArray(md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
328 | gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
329 | &Vlr_q);
| ~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp: In member function 'void gmx::EnergyOutput::addDataAtEnergyStep(bool, bool, double, real, const gmx_enerdata_t*, const t_state*, const t_lambda*, const t_expanded*, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const gmx_ekindata_t*, const real*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp:881:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
881 | add_ebin_indexed(ebin_, ie_, gmx::ArrayRef<bool>(bEner_), enerd->term, bSum);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:103:16: warning: ignoring return value of 'char* getenv(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
103 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:39:
/usr/include/c++/10/bits/unique_ptr.h: In function 'void init_forcerec(FILE*, const gmx::MDLogger&, t_forcerec*, t_fcdata*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, real (*)[3], const char*, const char*, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, const gmx_hw_info_t&, const gmx_device_info_t*, bool, bool, real, gmx_wallcycle*)':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function 'void gmx::lincs_update_atoms(gmx::Lincs*, int, real, gmx::ArrayRef<const double>, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*, real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:445:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
445 | static void lincs_update_atoms(Lincs* li,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:445:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp: In function 'void setCurrentLambdasLocal(int64_t, const t_lambda*, const double*, gmx::ArrayRef<double>, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:400:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
400 | void setCurrentLambdasLocal(const int64_t step,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function '_ZN3gmx15constrain_lincsEbRK10t_inputrecxPNS_5LincsERK9t_mdatomsPK9t_commrecPK14gmx_multisim_tPA3_KdPA3_dSI_SG_P5t_pbcdPddSI_bSI_NS_18ConstraintVariableEP6t_nrnbiPi._omp_fn.1':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:708:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
708 | lincs_update_atoms(lincsd, th, 1.0, sol, r,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
709 | (econq != ConstraintVariable::Force) ? invmass : nullptr, fp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:708:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function '_ZN3gmx15constrain_lincsEbRK10t_inputrecxPNS_5LincsERK9t_mdatomsPK9t_commrecPK14gmx_multisim_tPA3_KdPA3_dSI_SG_P5t_pbcdPddSI_bSI_NS_18ConstraintVariableEP6t_nrnbiPi._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1079:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1079 | lincs_update_atoms(lincsd, th, 1.0, mlambda, r, invmass, xp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1141:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1141 | lincs_update_atoms(lincsd, th, 1.0, blc_sol, r, invmass, xp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1148:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1148 | lincs_update_atoms(lincsd, th, invdt, mlambda, r, invmass, v);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function 'void atoms2md(const gmx_mtop_t*, const t_inputrec*, int, const int*, int, gmx::MDAtoms*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resize(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::set_lincs(const t_idef&, const t_mdatoms&, bool, const t_commrec*, gmx::Lincs*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, int, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:257:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
257 | void mdoutf_write_to_trajectory_files(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:282:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
282 | dd_collect_vec(cr->dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:287:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
287 | dd_collect_vec(cr->dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:293:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
293 | dd_collect_vec(cr->dd, state_local, f_local,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
294 | gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(f_global), f_local.size()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'int add_binr(t_bin*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
103 | int add_binr(t_bin* b, gmx::ArrayRef<const real> r)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'void extract_binr(t_bin*, int, gmx::ArrayRef<double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
160 | void extract_binr(t_bin* b, int index, gmx::ArrayRef<real> r)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, gmx::ImdSession*, pull_t*, int64_t, t_nrnb*, gmx_wallcycle_t, const gmx_localtop_t*, const real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, t_fcdata*, gmx::ArrayRef<double>, t_graph*, t_forcerec*, gmx::MdrunScheduleWorkload*, const gmx_vsite_t*, real*, double, gmx_edsam*, int, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:895:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
895 | void do_force(FILE* fplog,
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1070:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1070 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1103:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1103 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1154:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1154 | nbnxn_put_on_grid(nbv, box, 0, vzero, box_diag, nullptr, { 0, mdatoms->homenr }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1155 | fr->cginfo, x.unpaddedArrayRef(), 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1161:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1161 | nbnxn_put_on_grid_nonlocal(nbv, domdec_zones(cr->dd), fr->cginfo, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1243:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1243 | nbv->convertCoordinates(AtomLocality::Local, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1243:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1320:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1320 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1337:51: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1337 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1345:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1345 | nbv->convertCoordinates(AtomLocality::NonLocal, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1345:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1525:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1525 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
1526 | forceOut.forceWithShiftForces().shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1589:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1589 | stateGpu->copyForcesToGpu(forceOut.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1590 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1601:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1601 | stateGpu->copyForcesFromGpu(forceOut.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1602 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1613:57: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1613 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat, forceWithShiftForces.shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1634:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1634 | stateGpu->copyForcesToGpu(forceOut.forceWithShiftForces().force(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1771:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1771 | stateGpu->copyForcesToGpu(forceWithShift, locality);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1790:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1790 | stateGpu->copyForcesFromGpu(forceWithShift, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp: In function 'void do_md_trajectory_writing(FILE*, t_commrec*, int, const t_filenm*, int64_t, int64_t, double, t_inputrec*, t_state*, t_state*, ObservablesHistory*, const gmx_mtop_t*, t_forcerec*, gmx_mdoutf_t, const gmx::EnergyOutput&, gmx_ekindata_t*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:56:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
56 | void do_md_trajectory_writing(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:143:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
143 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step, t,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
144 | state, state_global, observablesHistory, f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp: In member function 'void gmx::UpdateConstrainCuda::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
70 | void UpdateConstrainCuda::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'void update_pcouple_after_coordinates(FILE*, int64_t, const t_inputrec*, const t_mdatoms*, const real (*)[3], const real (*)[3], const real (*)[3], real (*)[3], t_state*, t_nrnb*, gmx::Update*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1752:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1752 | upd->deform()->apply(localX, state->box, step);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'gmx_bool update_randomize_velocities(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, const gmx::Update*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1868:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1868 | extern gmx_bool update_randomize_velocities(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1896:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1896 | andersen_tcoupl(ir, step, cr, md, v, rate, upd->sd()->randomize_group, upd->sd()->boltzfac);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1896:24: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp: In member function 'void gmx::UpdateGroupsCog::addCogs(gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:80:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
80 | void UpdateGroupsCog::addCogs(gmx::ArrayRef<const int> globalAtomIndices,
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp: In function 'gmx::RangePartitioning gmx::makeUpdateGroups(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp:338:26: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
338 | static RangePartitioning makeUpdateGroups(const gmx_moltype_t& moltype, gmx::ArrayRef<const t_iparams> iparams)
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::Update::Impl::Impl(const t_inputrec*, gmx::BoxDeformation*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::Update::setNumAtoms(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void constructVsitesGlobal(const gmx_mtop_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:741:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
741 | void constructVsitesGlobal(const gmx_mtop_t& mtop, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:741:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual const std::vector<double>& gmx::{anonymous}::UnitAmplitudes::operator()(const t_mdatoms&, gmx::ArrayRef<const int>)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function '_Z25split_vsites_over_threadsPK7t_ilistPK9t_iparamsPK9t_mdatomsP11gmx_vsite_t._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp: In constructor 'gmx::DensityFittingForceProvider::Impl::Impl(const gmx::DensityFittingParameters&, gmx::basic_mdspan<const float, gmx::extents<-1, -1, -1> >, const gmx::TranslateAndScale&, const gmx::LocalAtomSet&, int, double, const gmx::DensityFittingForceProviderState&)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:79:19: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
79 | scaleToLattice({ &sigmaInLatticeCoordinates, &sigmaInLatticeCoordinates + 1 });
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:166:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
166 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
167 | { &referenceDensityCenter_, &referenceDensityCenter_ + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:171:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
171 | transformationToDensityLattice_({ &referenceDensityOriginShift, &referenceDensityOriginShift + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:172:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
172 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | { &referenceDensityOriginShift, &referenceDensityOriginShift + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp: In member function 'void gmx::DensityFittingForceProvider::Impl::calculateForces(const gmx::ForceProviderInput&, gmx::ForceProviderOutput*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:210:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
210 | transformationToDensityLattice_(transformedCoordinates_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:258:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
258 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(forces_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingparameters.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::BenchmarkSystem::BenchmarkSystem(int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:551:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
551 | static void pme_load_balance(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_loadbal_do(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, t_forcerec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_wallcycle_t, int64_t, int64_t, gmx_bool*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:896:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
896 | void pme_loadbal_do(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:1035:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1035 | pme_load_balance(pme_lb, cr, fp_err, fp_log, mdlog, ir, box, x,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1036 | pme_lb->cycles_c - cycles_prev, fr->ic, fr->nbv.get(), &fr->pmedata, step);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:104:16: warning: ignoring return value of 'char* getenv(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
104 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'void gmx_pme_calc_energy(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const double>, real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:952:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
952 | void gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q, real* V)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:952:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:72:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:72:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'int gmx_pmeonly(gmx_pme_t*, const t_commrec*, t_nrnb*, gmx_wallcycle*, gmx_walltime_accounting_t, t_inputrec*, PmeRunMode)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:711:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
711 | stateGpu->copyCoordinatesToGpu(gmx::ArrayRef<gmx::RVec>(pme_pp->x), gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
728 | gmx_pme_do(pme, pme_pp->x, pme_pp->f, pme_pp->chargeA.data(), pme_pp->chargeB.data(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
729 | pme_pp->sqrt_c6A.data(), pme_pp->sqrt_c6B.data(), pme_pp->sigmaA.data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
730 | pme_pp->sigmaB.data(), box, cr, maxshift_x, maxshift_y, mynrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
731 | output.coulombVirial_, output.lennardJonesVirial_, &output.coulombEnergy_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
732 | &output.lennardJonesEnergy_, lambda_q, lambda_lj, &dvdlambda_q,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
733 | &dvdlambda_lj, pmeFlags);
| ~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void dd_pmeredist_f(gmx_pme_t*, PmeAtomComm*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:388:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
388 | void dd_pmeredist_f(struct gmx_pme_t* pme, PmeAtomComm* atc, gmx::ArrayRef<gmx::RVec> f, gmx_bool bAddF)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'int gmx_pme_do(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, real*, real*, real*, real*, real*, real*, const real (*)[3], const t_commrec*, int, int, t_nrnb*, gmx_wallcycle*, real (*)[3], real (*)[3], real*, real*, real, real, real*, real*, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1004:5: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1004 | int gmx_pme_do(struct gmx_pme_t* pme,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1004:5: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1154:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1154 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, coefficient);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1154:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1384:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1384 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, RedistC6);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1384:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1393:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1393 | do_redist_pos_coeffs(pme, cr, FALSE, coordinates, RedistSigma);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1393:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void do_redist_pos_coeffs(gmx_pme_t*, const t_commrec*, gmx_bool, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:453:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
453 | void do_redist_pos_coeffs(struct gmx_pme_t* pme,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_testutils.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:545:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
545 | dd_collect_vec(cr->dd, &state->s, state->s.x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp: In member function 'void gmx::LegacySimulator::do_mimic()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:227:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
227 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:379:35: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
379 | setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:421:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
421 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
422 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
423 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
424 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
425 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
426 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:437:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
437 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
438 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
439 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
440 | fr, runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
441 | ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:451:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
451 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
452 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
453 | energyOutput, ekind, f, isCheckpointingStep, doRerun,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
454 | isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:509:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
509 | dd_collect_vec(cr->dd, state, flocal, ftemp);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:519:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
519 | mimicCommunicator.sendForces(ftemp, state_global->natoms);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:533:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
533 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void {anonymous}::EnergyEvaluator::run(em_state_t*, real*, real (*)[3], real (*)[3], int64_t, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:845:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
845 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, count, nrnb, wcycle,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
846 | top, ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
847 | ems->f.arrayRefWithPadding(), force_vir, mdAtoms->mdatoms(), enerd, fcd, ems->s.lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
848 | graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
849 | GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES | GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
850 | | (bNS ? GMX_FORCE_NS : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
851 | DDBalanceRegionHandler(cr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:905:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
905 | sum_dhdl(enerd, ems->s.lambda, *inputrec->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
253 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:749:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
749 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:753:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
753 | pme_loadbal_do(pme_loadbal, cr, (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
754 | fplog, mdlog, *ir, fr, state->box, state->x, wcycle, step, step_rel,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
755 | &bPMETunePrinting, simulationWork.useGpuPmePpCommunication);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:767:35: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
767 | setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:810:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
810 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:815:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
815 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:918:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
918 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
919 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
920 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
921 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
922 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
923 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:945:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
945 | do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
946 | nrnb, wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
947 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
948 | fr, runScheduleWork, vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
949 | (bNS ? GMX_FORCE_NS : 0) | force_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1100:25: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1100 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1128:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1128 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1136:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1136 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1152:40: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1152 | stateGpu->copyForcesFromGpu(ArrayRef<RVec>(f), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1159:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1159 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1160 | observablesHistory, top_global, fr, outf, energyOutput, ekind, f,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1161 | checkpointHandler->isCheckpointingStep(), bRerunMD, bLastStep,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1162 | mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1194:55: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1194 | bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, &upd, constr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1266:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1266 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1267:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1267 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1273:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1273 | stateGpu->copyForcesToGpu(ArrayRef<RVec>(f), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1280:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1280 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1281 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1282 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1283 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1290:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1290 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1393:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1393 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1429:55: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1429 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1437:58: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1437 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1455:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1455 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'bool do_em_step(const t_commrec*, t_inputrec*, t_mdatoms*, em_state_t*, real, PaddedHostVector<gmx::BasicVector<double> >*, em_state_t*, gmx::Constraints*, int64_t)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void init_em(FILE*, const gmx::MDLogger&, const char*, const t_commrec*, t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, gmx_mtop_t*, em_state_t*, gmx_localtop_t*, t_nrnb*, t_forcerec*, t_graph**, gmx::MDAtoms*, gmx_global_stat**, gmx_vsite_t*, gmx::Constraints*, gmx_shellfc_t**)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:385:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
385 | initialize_lambdas(fplog, *ir, MASTER(cr), &(state_global->fep_state), state_global->lambda, nullptr);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_lbfgs()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1858:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1858 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1859 | static_cast<real>(step), &ems.s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1860 | observablesHistory, ems.f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:52:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp: In member function 'void gmx::LegacySimulator::do_rerun()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:302:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
302 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:52:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:551:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
551 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
552 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
553 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
554 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
555 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
556 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:567:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
567 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
568 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
569 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
570 | fr, runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
571 | ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:581:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
581 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
582 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
583 | energyOutput, ekind, f, isCheckpointingStep, doRerun,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
584 | isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:641:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
641 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_nm()':
/<<PKGBUILDDIR>>